Starting phenix.real_space_refine on Sat Mar 16 01:07:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoy_33363/03_2024/7xoy_33363_trim_updated.pdb" } resolution = 4.25 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= 0.004 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 4 5.49 5 S 52 5.16 5 C 8336 2.51 5 N 2336 2.21 5 O 2536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 96": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13264 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Time building chain proxies: 6.86, per 1000 atoms: 0.52 Number of scatterers: 13264 At special positions: 0 Unit cell: (104.13, 143.91, 81.9, 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 52 16.00 P 4 15.00 O 2536 8.00 N 2336 7.00 C 8336 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 2.5 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 20 sheets defined 38.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'B' and resid 7 through 10 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.516A pdb=" N LYS B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.618A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.913A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 249 through 262 removed outlier: 4.000A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 283 removed outlier: 3.979A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 3.705A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 423 through 432 removed outlier: 4.633A pdb=" N ASP B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.540A pdb=" N ARG A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.606A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.914A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.999A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 4.179A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.706A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 423 through 432 removed outlier: 4.633A pdb=" N ASP A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'C' and resid 7 through 10 Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.575A pdb=" N ARG C 46 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.592A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.602A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 184 through 197 removed outlier: 4.880A pdb=" N ALA C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 194 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 196 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 249 through 262 removed outlier: 4.017A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 283 removed outlier: 4.187A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 3.670A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 330 through 335 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 423 through 432 removed outlier: 4.645A pdb=" N ASP C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 Processing helix chain 'D' and resid 7 through 10 Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.569A pdb=" N ARG D 46 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.621A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 184 through 197 removed outlier: 4.636A pdb=" N ALA D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 196 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'D' and resid 249 through 262 removed outlier: 4.017A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 283 removed outlier: 4.185A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 3.667A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 389 through 395 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 423 through 432 removed outlier: 4.642A pdb=" N ASP D 432 " --> pdb=" O LYS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 459 Processing sheet with id= A, first strand: chain 'B' and resid 16 through 18 removed outlier: 5.848A pdb=" N ILE B 290 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS B 33 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 292 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.400A pdb=" N LYS B 89 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU B 69 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 91 " --> pdb=" O GLU B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 204 through 208 removed outlier: 7.194A pdb=" N GLU B 242 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP B 207 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 244 " --> pdb=" O ASP B 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 367 through 370 Processing sheet with id= E, first strand: chain 'B' and resid 435 through 439 Processing sheet with id= F, first strand: chain 'A' and resid 16 through 18 removed outlier: 5.896A pdb=" N ILE A 290 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS A 33 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 292 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.402A pdb=" N LYS A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A 69 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 91 " --> pdb=" O GLU A 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 204 through 208 removed outlier: 7.195A pdb=" N GLU A 242 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASP A 207 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 244 " --> pdb=" O ASP A 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 367 through 370 Processing sheet with id= J, first strand: chain 'A' and resid 435 through 439 Processing sheet with id= K, first strand: chain 'C' and resid 16 through 18 removed outlier: 5.872A pdb=" N ILE C 290 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS C 33 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 292 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 66 through 69 removed outlier: 6.407A pdb=" N LYS C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLU C 69 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 91 " --> pdb=" O GLU C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 204 through 208 removed outlier: 7.196A pdb=" N GLU C 242 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASP C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 244 " --> pdb=" O ASP C 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 367 through 370 Processing sheet with id= O, first strand: chain 'C' and resid 435 through 439 Processing sheet with id= P, first strand: chain 'D' and resid 16 through 18 removed outlier: 5.871A pdb=" N ILE D 290 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS D 33 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 292 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 66 through 69 removed outlier: 6.404A pdb=" N LYS D 89 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLU D 69 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 91 " --> pdb=" O GLU D 69 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 204 through 208 removed outlier: 7.193A pdb=" N GLU D 242 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ASP D 207 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 244 " --> pdb=" O ASP D 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 367 through 370 Processing sheet with id= T, first strand: chain 'D' and resid 435 through 439 402 hydrogen bonds defined for protein. 990 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: 3.79 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2830 1.33 - 1.45: 2924 1.45 - 1.57: 7690 1.57 - 1.69: 4 1.69 - 1.81: 88 Bond restraints: 13536 Sorted by residual: bond pdb=" C PRO A 70 " pdb=" O PRO A 70 " ideal model delta sigma weight residual 1.235 1.205 0.030 7.90e-03 1.60e+04 1.41e+01 bond pdb=" N ILE B 180 " pdb=" CA ILE B 180 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.79e+00 bond pdb=" N VAL B 98 " pdb=" CA VAL B 98 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.57e+00 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.47e+00 bond pdb=" N VAL D 98 " pdb=" CA VAL D 98 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.39e+00 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 567 106.64 - 113.48: 7431 113.48 - 120.32: 5052 120.32 - 127.17: 5235 127.17 - 134.01: 155 Bond angle restraints: 18440 Sorted by residual: angle pdb=" C GLY C 76 " pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta sigma weight residual 120.88 113.82 7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N THR C 75 " pdb=" CA THR C 75 " pdb=" C THR C 75 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.58e+01 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.18 107.49 5.69 1.21e+00 6.83e-01 2.21e+01 angle pdb=" N THR C 182 " pdb=" CA THR C 182 " pdb=" C THR C 182 " ideal model delta sigma weight residual 113.19 107.76 5.43 1.19e+00 7.06e-01 2.08e+01 angle pdb=" C ALA C 343 " pdb=" CA ALA C 343 " pdb=" CB ALA C 343 " ideal model delta sigma weight residual 116.54 111.46 5.08 1.15e+00 7.56e-01 1.95e+01 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 7765 28.61 - 57.23: 246 57.23 - 85.84: 17 85.84 - 114.45: 0 114.45 - 143.07: 4 Dihedral angle restraints: 8032 sinusoidal: 2928 harmonic: 5104 Sorted by residual: dihedral pdb=" CB PLS B 501 " pdb=" N PLS B 501 " pdb=" CA PLS B 501 " pdb=" C4A PLS B 501 " ideal model delta sinusoidal sigma weight residual -168.88 -25.81 -143.07 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CB PLS C 601 " pdb=" N PLS C 601 " pdb=" CA PLS C 601 " pdb=" C4A PLS C 601 " ideal model delta sinusoidal sigma weight residual -168.88 -25.83 -143.05 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CB PLS A 501 " pdb=" N PLS A 501 " pdb=" CA PLS A 501 " pdb=" C4A PLS A 501 " ideal model delta sinusoidal sigma weight residual -168.88 -25.88 -143.00 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 8029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1478 0.052 - 0.103: 481 0.103 - 0.155: 82 0.155 - 0.206: 20 0.206 - 0.258: 7 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2065 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 277 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ALA D 277 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA D 277 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU D 278 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 277 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ALA C 277 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA C 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 278 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 277 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA A 277 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA A 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3575 2.78 - 3.31: 14484 3.31 - 3.84: 21803 3.84 - 4.37: 25295 4.37 - 4.90: 39690 Nonbonded interactions: 104847 Sorted by model distance: nonbonded pdb=" N GLN C 147 " pdb=" OE1 GLN C 147 " model vdw 2.255 2.520 nonbonded pdb=" N GLN D 147 " pdb=" OE1 GLN D 147 " model vdw 2.261 2.520 nonbonded pdb=" N LYS B 401 " pdb=" OD2 ASP B 404 " model vdw 2.274 2.520 nonbonded pdb=" N LYS A 401 " pdb=" OD2 ASP A 404 " model vdw 2.277 2.520 nonbonded pdb=" OD1 ASP D 250 " pdb=" NH1 ARG D 318 " model vdw 2.278 2.520 ... (remaining 104842 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 3.810 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 38.320 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.006 0.037 13536 Z= 0.434 Angle : 0.732 7.064 18440 Z= 0.467 Chirality : 0.053 0.258 2068 Planarity : 0.004 0.041 2440 Dihedral : 13.204 143.067 4816 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 45.15 Ramachandran Plot: Outliers : 1.15 % Allowed : 10.20 % Favored : 88.65 % Rotamer: Outliers : 8.23 % Allowed : 7.76 % Favored : 84.01 % 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: -2.66 (0.20), residues: 1824 helix: -0.75 (0.20), residues: 700 sheet: -2.22 (0.39), residues: 176 loop : -2.52 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS A 348 PHE 0.011 0.001 PHE C 316 TYR 0.011 0.001 TYR A 451 ARG 0.002 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 310 time to evaluate : 1.582 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: B 157 HIS cc_start: 0.8743 (m-70) cc_final: 0.8501 (m-70) REVERT: B 316 PHE cc_start: 0.8906 (p90) cc_final: 0.8401 (p90) REVERT: A 97 LYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4422 (mptt) REVERT: A 316 PHE cc_start: 0.8824 (p90) cc_final: 0.8314 (p90) REVERT: C 38 ASN cc_start: 0.9366 (m-40) cc_final: 0.8710 (m-40) REVERT: C 224 GLU cc_start: 0.8923 (tt0) cc_final: 0.8431 (mp0) REVERT: C 368 MET cc_start: 0.8913 (ptm) cc_final: 0.8291 (ptm) REVERT: C 456 PHE cc_start: 0.8550 (t80) cc_final: 0.7677 (t80) REVERT: D 38 ASN cc_start: 0.9334 (m-40) cc_final: 0.8690 (m-40) REVERT: D 112 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7303 (mt-10) REVERT: D 185 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8280 (m) REVERT: D 224 GLU cc_start: 0.8978 (tt0) cc_final: 0.8509 (mp0) REVERT: D 368 MET cc_start: 0.8722 (ptm) cc_final: 0.8271 (ptm) outliers start: 106 outliers final: 24 residues processed: 380 average time/residue: 0.2865 time to fit residues: 149.3637 Evaluate side-chains 225 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13536 Z= 0.243 Angle : 0.686 9.471 18440 Z= 0.346 Chirality : 0.046 0.193 2068 Planarity : 0.006 0.045 2440 Dihedral : 8.340 156.168 2020 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.66 % Favored : 91.17 % Rotamer: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.57 % 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: -2.48 (0.20), residues: 1824 helix: -0.84 (0.19), residues: 712 sheet: -2.55 (0.34), residues: 204 loop : -2.06 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 143 HIS 0.006 0.001 HIS D 157 PHE 0.016 0.002 PHE B 230 TYR 0.018 0.001 TYR D 451 ARG 0.006 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.591 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: B 20 ASN cc_start: 0.8062 (m-40) cc_final: 0.7855 (m-40) REVERT: B 38 ASN cc_start: 0.8714 (t0) cc_final: 0.8375 (t0) REVERT: B 45 ASP cc_start: 0.8771 (p0) cc_final: 0.8349 (p0) REVERT: B 51 MET cc_start: 0.9138 (mtm) cc_final: 0.8778 (mtm) REVERT: B 52 ILE cc_start: 0.9327 (mm) cc_final: 0.9111 (mm) REVERT: B 61 LEU cc_start: 0.7915 (tt) cc_final: 0.7401 (mm) REVERT: B 168 ASP cc_start: 0.8285 (m-30) cc_final: 0.8066 (m-30) REVERT: B 207 ASP cc_start: 0.8599 (t0) cc_final: 0.8385 (t0) REVERT: B 307 ASN cc_start: 0.8737 (t0) cc_final: 0.8491 (t0) REVERT: B 311 MET cc_start: 0.9051 (tpp) cc_final: 0.8409 (tpp) REVERT: B 336 ARG cc_start: 0.6183 (tpt170) cc_final: 0.5947 (tpt170) REVERT: A 20 ASN cc_start: 0.8017 (m-40) cc_final: 0.7771 (m-40) REVERT: A 52 ILE cc_start: 0.9290 (mm) cc_final: 0.9080 (mm) REVERT: A 168 ASP cc_start: 0.8280 (m-30) cc_final: 0.8041 (m-30) REVERT: A 224 GLU cc_start: 0.8146 (tp30) cc_final: 0.7941 (tp30) REVERT: A 307 ASN cc_start: 0.8695 (t0) cc_final: 0.8469 (t0) REVERT: A 311 MET cc_start: 0.9112 (tpp) cc_final: 0.8458 (tpp) REVERT: A 341 LEU cc_start: 0.8284 (tt) cc_final: 0.7754 (tt) REVERT: C 224 GLU cc_start: 0.8801 (tt0) cc_final: 0.8442 (mp0) REVERT: C 368 MET cc_start: 0.8944 (ptm) cc_final: 0.8233 (ptm) REVERT: C 451 TYR cc_start: 0.8793 (t80) cc_final: 0.8590 (t80) REVERT: C 456 PHE cc_start: 0.8109 (t80) cc_final: 0.7677 (t80) REVERT: D 112 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7223 (mt-10) REVERT: D 224 GLU cc_start: 0.8752 (tt0) cc_final: 0.8399 (mp0) REVERT: D 228 GLU cc_start: 0.7570 (tp30) cc_final: 0.7349 (tp30) REVERT: D 272 MET cc_start: 0.8844 (ttt) cc_final: 0.8517 (tmm) REVERT: D 456 PHE cc_start: 0.8209 (t80) cc_final: 0.7670 (t80) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.2545 time to fit residues: 91.3120 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.1972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13536 Z= 0.213 Angle : 0.627 7.795 18440 Z= 0.317 Chirality : 0.045 0.201 2068 Planarity : 0.005 0.049 2440 Dihedral : 8.340 152.132 2020 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -2.13 (0.20), residues: 1824 helix: -0.63 (0.19), residues: 716 sheet: -2.30 (0.31), residues: 252 loop : -1.74 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 143 HIS 0.003 0.001 HIS A 348 PHE 0.013 0.002 PHE C 316 TYR 0.013 0.001 TYR D 36 ARG 0.003 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.634 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: B 52 ILE cc_start: 0.9334 (mm) cc_final: 0.9050 (mm) REVERT: B 254 MET cc_start: 0.8856 (tpp) cc_final: 0.8582 (tpp) REVERT: B 264 MET cc_start: 0.9014 (mmm) cc_final: 0.8809 (mmm) REVERT: B 307 ASN cc_start: 0.8600 (t0) cc_final: 0.8353 (t0) REVERT: B 311 MET cc_start: 0.9014 (tpp) cc_final: 0.8396 (tpp) REVERT: B 368 MET cc_start: 0.8103 (ttm) cc_final: 0.7792 (ttp) REVERT: B 385 SER cc_start: 0.7979 (m) cc_final: 0.7753 (m) REVERT: A 20 ASN cc_start: 0.7909 (m-40) cc_final: 0.7639 (m-40) REVERT: A 45 ASP cc_start: 0.8582 (p0) cc_final: 0.8185 (p0) REVERT: A 224 GLU cc_start: 0.8117 (tp30) cc_final: 0.7878 (tm-30) REVERT: A 307 ASN cc_start: 0.8610 (t0) cc_final: 0.8374 (t0) REVERT: A 311 MET cc_start: 0.9073 (tpp) cc_final: 0.8352 (tpp) REVERT: A 368 MET cc_start: 0.8337 (ttp) cc_final: 0.8112 (tmm) REVERT: C 84 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8389 (mm-40) REVERT: C 224 GLU cc_start: 0.8835 (tt0) cc_final: 0.8414 (mp0) REVERT: C 272 MET cc_start: 0.8773 (ttp) cc_final: 0.8427 (tmm) REVERT: C 410 MET cc_start: 0.8265 (ptm) cc_final: 0.7975 (ptm) REVERT: C 451 TYR cc_start: 0.8873 (t80) cc_final: 0.8660 (t80) REVERT: C 456 PHE cc_start: 0.8088 (t80) cc_final: 0.7639 (t80) REVERT: D 35 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 38 ASN cc_start: 0.9261 (m-40) cc_final: 0.8719 (m110) REVERT: D 224 GLU cc_start: 0.8755 (tt0) cc_final: 0.8300 (mp0) REVERT: D 228 GLU cc_start: 0.7522 (tp30) cc_final: 0.7321 (tp30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2368 time to fit residues: 80.0196 Evaluate side-chains 176 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 0.2980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13536 Z= 0.210 Angle : 0.615 8.102 18440 Z= 0.311 Chirality : 0.045 0.161 2068 Planarity : 0.005 0.046 2440 Dihedral : 8.041 146.852 2020 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -1.96 (0.20), residues: 1824 helix: -0.74 (0.18), residues: 760 sheet: -1.76 (0.35), residues: 224 loop : -1.60 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.003 0.001 HIS C 348 PHE 0.012 0.002 PHE B 316 TYR 0.015 0.001 TYR A 213 ARG 0.003 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.7605 (m-40) cc_final: 0.7341 (m-40) REVERT: B 45 ASP cc_start: 0.9039 (p0) cc_final: 0.8681 (p0) REVERT: B 254 MET cc_start: 0.8861 (tpp) cc_final: 0.8580 (tpp) REVERT: B 307 ASN cc_start: 0.8524 (t0) cc_final: 0.8226 (t0) REVERT: B 351 GLU cc_start: 0.8373 (tt0) cc_final: 0.8107 (tt0) REVERT: B 368 MET cc_start: 0.8048 (ttm) cc_final: 0.7819 (ttp) REVERT: A 20 ASN cc_start: 0.8194 (m-40) cc_final: 0.7852 (m-40) REVERT: A 51 MET cc_start: 0.8949 (mtm) cc_final: 0.8707 (mtm) REVERT: A 264 MET cc_start: 0.8903 (mmm) cc_final: 0.8614 (mtp) REVERT: A 307 ASN cc_start: 0.8522 (t0) cc_final: 0.8208 (t0) REVERT: A 311 MET cc_start: 0.8942 (tpp) cc_final: 0.8219 (tpp) REVERT: A 368 MET cc_start: 0.8158 (ttp) cc_final: 0.7838 (tmm) REVERT: C 112 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 209 GLU cc_start: 0.7518 (pm20) cc_final: 0.7263 (pm20) REVERT: C 224 GLU cc_start: 0.8834 (tt0) cc_final: 0.8435 (mp0) REVERT: D 38 ASN cc_start: 0.9261 (m-40) cc_final: 0.8530 (m110) REVERT: D 44 LYS cc_start: 0.8384 (tttt) cc_final: 0.8166 (ttmt) REVERT: D 166 TRP cc_start: 0.9108 (t-100) cc_final: 0.8628 (t-100) REVERT: D 224 GLU cc_start: 0.8656 (tt0) cc_final: 0.8337 (mp0) REVERT: D 228 GLU cc_start: 0.7606 (tp30) cc_final: 0.7376 (tp30) REVERT: D 264 MET cc_start: 0.8991 (mmm) cc_final: 0.8634 (mtp) REVERT: D 272 MET cc_start: 0.8965 (ttp) cc_final: 0.8693 (tmm) REVERT: D 410 MET cc_start: 0.8145 (ptm) cc_final: 0.7937 (ptm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2388 time to fit residues: 76.4866 Evaluate side-chains 179 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13536 Z= 0.391 Angle : 0.716 9.123 18440 Z= 0.363 Chirality : 0.047 0.177 2068 Planarity : 0.006 0.044 2440 Dihedral : 8.472 158.697 2020 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.70 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -2.07 (0.20), residues: 1824 helix: -0.87 (0.18), residues: 756 sheet: -1.52 (0.33), residues: 264 loop : -1.71 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 433 HIS 0.007 0.001 HIS A 157 PHE 0.014 0.002 PHE D 316 TYR 0.017 0.001 TYR D 36 ARG 0.004 0.001 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.7951 (m-40) cc_final: 0.7707 (m-40) REVERT: B 44 LYS cc_start: 0.8705 (tptt) cc_final: 0.8498 (tptm) REVERT: B 61 LEU cc_start: 0.7942 (tt) cc_final: 0.7700 (mm) REVERT: B 72 SER cc_start: 0.8400 (m) cc_final: 0.8093 (t) REVERT: B 254 MET cc_start: 0.8991 (tpp) cc_final: 0.8647 (tpp) REVERT: B 351 GLU cc_start: 0.8352 (tt0) cc_final: 0.8108 (tt0) REVERT: A 20 ASN cc_start: 0.8311 (m-40) cc_final: 0.8045 (m-40) REVERT: A 61 LEU cc_start: 0.8104 (tt) cc_final: 0.7730 (mm) REVERT: A 311 MET cc_start: 0.9052 (tpp) cc_final: 0.8410 (tpp) REVERT: A 368 MET cc_start: 0.8391 (ttp) cc_final: 0.7904 (tmm) REVERT: C 38 ASN cc_start: 0.9178 (m-40) cc_final: 0.8961 (t0) REVERT: C 45 ASP cc_start: 0.8644 (p0) cc_final: 0.7915 (p0) REVERT: C 112 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 209 GLU cc_start: 0.7648 (pm20) cc_final: 0.7212 (pm20) REVERT: C 367 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7922 (tp40) REVERT: C 451 TYR cc_start: 0.8951 (t80) cc_final: 0.8521 (t80) REVERT: D 35 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7574 (mm-30) REVERT: D 38 ASN cc_start: 0.9263 (m-40) cc_final: 0.8409 (m110) REVERT: D 44 LYS cc_start: 0.8489 (tttt) cc_final: 0.8284 (tttt) REVERT: D 228 GLU cc_start: 0.7567 (tp30) cc_final: 0.7360 (tp30) REVERT: D 264 MET cc_start: 0.9144 (mmm) cc_final: 0.8930 (mtp) REVERT: D 368 MET cc_start: 0.8639 (ptm) cc_final: 0.8426 (ptm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2195 time to fit residues: 65.6862 Evaluate side-chains 164 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.0040 chunk 91 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13536 Z= 0.189 Angle : 0.602 8.264 18440 Z= 0.305 Chirality : 0.044 0.172 2068 Planarity : 0.005 0.046 2440 Dihedral : 7.764 149.355 2020 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.57 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.66 (0.20), residues: 1824 helix: -0.50 (0.19), residues: 752 sheet: -1.18 (0.34), residues: 264 loop : -1.56 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.004 0.001 HIS A 348 PHE 0.021 0.002 PHE C 316 TYR 0.017 0.001 TYR D 451 ARG 0.003 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.610 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: B 11 ILE cc_start: 0.8877 (mt) cc_final: 0.8673 (mt) REVERT: B 20 ASN cc_start: 0.7990 (m-40) cc_final: 0.7463 (m-40) REVERT: B 52 ILE cc_start: 0.9256 (mm) cc_final: 0.9037 (mm) REVERT: B 61 LEU cc_start: 0.8053 (tt) cc_final: 0.7600 (mm) REVERT: B 72 SER cc_start: 0.8387 (m) cc_final: 0.8096 (t) REVERT: B 254 MET cc_start: 0.8924 (tpp) cc_final: 0.8622 (tpp) REVERT: B 307 ASN cc_start: 0.8486 (t0) cc_final: 0.8110 (t0) REVERT: A 20 ASN cc_start: 0.8333 (m-40) cc_final: 0.7923 (m-40) REVERT: A 307 ASN cc_start: 0.8475 (t0) cc_final: 0.8055 (t0) REVERT: A 311 MET cc_start: 0.9029 (tpp) cc_final: 0.8351 (tpp) REVERT: A 368 MET cc_start: 0.8290 (ttp) cc_final: 0.8020 (tmm) REVERT: A 404 ASP cc_start: 0.8198 (m-30) cc_final: 0.7621 (t70) REVERT: C 45 ASP cc_start: 0.8616 (p0) cc_final: 0.7911 (p0) REVERT: C 112 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 451 TYR cc_start: 0.8805 (t80) cc_final: 0.8486 (t80) REVERT: D 44 LYS cc_start: 0.8488 (tttt) cc_final: 0.8236 (tttt) REVERT: D 228 GLU cc_start: 0.7533 (tp30) cc_final: 0.7318 (tp30) REVERT: D 254 MET cc_start: 0.8879 (tpp) cc_final: 0.8651 (tpp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2166 time to fit residues: 68.5461 Evaluate side-chains 166 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 chunk 98 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13536 Z= 0.168 Angle : 0.599 8.263 18440 Z= 0.301 Chirality : 0.044 0.175 2068 Planarity : 0.005 0.047 2440 Dihedral : 7.441 139.286 2020 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -1.44 (0.20), residues: 1824 helix: -0.38 (0.19), residues: 748 sheet: -0.65 (0.36), residues: 232 loop : -1.52 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS A 409 PHE 0.020 0.002 PHE C 316 TYR 0.007 0.001 TYR A 451 ARG 0.002 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ILE cc_start: 0.8730 (mt) cc_final: 0.8430 (mm) REVERT: B 20 ASN cc_start: 0.7683 (m-40) cc_final: 0.7410 (m-40) REVERT: B 61 LEU cc_start: 0.8036 (tt) cc_final: 0.7573 (mm) REVERT: B 254 MET cc_start: 0.8946 (tpp) cc_final: 0.8688 (tpp) REVERT: B 272 MET cc_start: 0.8517 (tmm) cc_final: 0.8050 (tmm) REVERT: B 307 ASN cc_start: 0.8453 (t0) cc_final: 0.8132 (t0) REVERT: B 430 LEU cc_start: 0.9266 (mp) cc_final: 0.9058 (mp) REVERT: A 11 ILE cc_start: 0.8703 (mt) cc_final: 0.8447 (mt) REVERT: A 20 ASN cc_start: 0.8068 (m-40) cc_final: 0.7844 (m-40) REVERT: A 307 ASN cc_start: 0.8463 (t0) cc_final: 0.8172 (t0) REVERT: A 311 MET cc_start: 0.9002 (tpp) cc_final: 0.8305 (tpp) REVERT: A 368 MET cc_start: 0.8356 (ttp) cc_final: 0.8011 (tmm) REVERT: A 404 ASP cc_start: 0.8096 (m-30) cc_final: 0.7578 (t70) REVERT: C 45 ASP cc_start: 0.8356 (p0) cc_final: 0.8151 (p0) REVERT: C 112 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7468 (mt-10) REVERT: C 192 TYR cc_start: 0.8611 (t80) cc_final: 0.8349 (t80) REVERT: C 451 TYR cc_start: 0.8760 (t80) cc_final: 0.8492 (t80) REVERT: D 38 ASN cc_start: 0.9233 (m-40) cc_final: 0.8494 (m110) REVERT: D 146 ASP cc_start: 0.7608 (t0) cc_final: 0.7405 (t0) REVERT: D 228 GLU cc_start: 0.7499 (tp30) cc_final: 0.7273 (tp30) REVERT: D 254 MET cc_start: 0.8819 (tpp) cc_final: 0.8606 (tpp) REVERT: D 272 MET cc_start: 0.8668 (ttp) cc_final: 0.8348 (tmm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2305 time to fit residues: 75.0787 Evaluate side-chains 168 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13536 Z= 0.374 Angle : 0.719 13.512 18440 Z= 0.363 Chirality : 0.048 0.186 2068 Planarity : 0.006 0.060 2440 Dihedral : 8.396 176.102 2020 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.48 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.63 (0.20), residues: 1824 helix: -0.61 (0.18), residues: 756 sheet: -0.48 (0.38), residues: 224 loop : -1.62 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 433 HIS 0.008 0.001 HIS B 348 PHE 0.025 0.002 PHE B 316 TYR 0.017 0.001 TYR C 128 ARG 0.004 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.7774 (m-40) cc_final: 0.7565 (m-40) REVERT: B 51 MET cc_start: 0.9211 (mtm) cc_final: 0.8897 (mtm) REVERT: B 61 LEU cc_start: 0.8214 (tt) cc_final: 0.7742 (mm) REVERT: B 254 MET cc_start: 0.8978 (tpp) cc_final: 0.8628 (tpp) REVERT: A 11 ILE cc_start: 0.8895 (mt) cc_final: 0.8650 (mt) REVERT: A 20 ASN cc_start: 0.8171 (m-40) cc_final: 0.7736 (m-40) REVERT: A 311 MET cc_start: 0.9051 (tpp) cc_final: 0.8312 (tpp) REVERT: A 368 MET cc_start: 0.8329 (ttp) cc_final: 0.8045 (tmm) REVERT: C 38 ASN cc_start: 0.8985 (t0) cc_final: 0.8509 (t0) REVERT: C 45 ASP cc_start: 0.8381 (p0) cc_final: 0.7990 (p0) REVERT: C 112 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 451 TYR cc_start: 0.8937 (t80) cc_final: 0.8392 (t80) REVERT: D 38 ASN cc_start: 0.9266 (m-40) cc_final: 0.8523 (m110) REVERT: D 228 GLU cc_start: 0.7492 (tp30) cc_final: 0.7283 (tp30) REVERT: D 264 MET cc_start: 0.9096 (mmm) cc_final: 0.8865 (mtp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2084 time to fit residues: 57.2994 Evaluate side-chains 142 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13536 Z= 0.184 Angle : 0.621 7.898 18440 Z= 0.311 Chirality : 0.044 0.149 2068 Planarity : 0.005 0.052 2440 Dihedral : 7.906 157.238 2020 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1824 helix: -0.34 (0.19), residues: 752 sheet: -0.38 (0.37), residues: 232 loop : -1.46 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS A 348 PHE 0.024 0.002 PHE A 316 TYR 0.009 0.001 TYR A 451 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ILE cc_start: 0.8875 (mt) cc_final: 0.8646 (mm) REVERT: B 72 SER cc_start: 0.8597 (m) cc_final: 0.7998 (t) REVERT: B 254 MET cc_start: 0.8914 (tpp) cc_final: 0.8604 (tpp) REVERT: B 307 ASN cc_start: 0.8509 (t0) cc_final: 0.8147 (t0) REVERT: B 404 ASP cc_start: 0.8205 (m-30) cc_final: 0.7787 (t70) REVERT: A 11 ILE cc_start: 0.8862 (mt) cc_final: 0.8615 (mt) REVERT: A 20 ASN cc_start: 0.8194 (m-40) cc_final: 0.7743 (m-40) REVERT: A 307 ASN cc_start: 0.8518 (t0) cc_final: 0.8194 (t0) REVERT: A 311 MET cc_start: 0.8986 (tpp) cc_final: 0.8468 (tpp) REVERT: A 368 MET cc_start: 0.8351 (ttp) cc_final: 0.8079 (tmm) REVERT: A 404 ASP cc_start: 0.8064 (m-30) cc_final: 0.7733 (t70) REVERT: C 38 ASN cc_start: 0.8973 (t0) cc_final: 0.8488 (t0) REVERT: C 45 ASP cc_start: 0.8314 (p0) cc_final: 0.7836 (p0) REVERT: C 112 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7428 (mt-10) REVERT: C 192 TYR cc_start: 0.8632 (t80) cc_final: 0.8379 (t80) REVERT: C 254 MET cc_start: 0.8885 (tpp) cc_final: 0.8491 (tpp) REVERT: C 451 TYR cc_start: 0.8806 (t80) cc_final: 0.8352 (t80) REVERT: D 38 ASN cc_start: 0.9255 (m-40) cc_final: 0.8562 (m110) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2219 time to fit residues: 63.9520 Evaluate side-chains 159 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS C 367 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13536 Z= 0.206 Angle : 0.623 8.850 18440 Z= 0.313 Chirality : 0.044 0.156 2068 Planarity : 0.005 0.053 2440 Dihedral : 7.864 164.925 2020 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1824 helix: -0.31 (0.19), residues: 760 sheet: -0.28 (0.37), residues: 232 loop : -1.47 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS C 348 PHE 0.024 0.002 PHE A 316 TYR 0.010 0.001 TYR C 36 ARG 0.003 0.000 ARG D 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ILE cc_start: 0.8931 (mt) cc_final: 0.8730 (mm) REVERT: B 72 SER cc_start: 0.8593 (m) cc_final: 0.7948 (t) REVERT: B 254 MET cc_start: 0.8914 (tpp) cc_final: 0.8617 (tpp) REVERT: B 307 ASN cc_start: 0.8521 (t0) cc_final: 0.8191 (t0) REVERT: B 404 ASP cc_start: 0.8246 (m-30) cc_final: 0.7775 (t70) REVERT: A 20 ASN cc_start: 0.8092 (m-40) cc_final: 0.7662 (m-40) REVERT: A 264 MET cc_start: 0.8611 (mmm) cc_final: 0.8304 (mtp) REVERT: A 307 ASN cc_start: 0.8508 (t0) cc_final: 0.8111 (t0) REVERT: A 368 MET cc_start: 0.8340 (ttp) cc_final: 0.7977 (tmm) REVERT: A 404 ASP cc_start: 0.8071 (m-30) cc_final: 0.7743 (t70) REVERT: C 38 ASN cc_start: 0.9009 (t0) cc_final: 0.8537 (t0) REVERT: C 45 ASP cc_start: 0.8296 (p0) cc_final: 0.7830 (p0) REVERT: C 112 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 192 TYR cc_start: 0.8640 (t80) cc_final: 0.8399 (t80) REVERT: C 451 TYR cc_start: 0.8810 (t80) cc_final: 0.8350 (t80) REVERT: D 38 ASN cc_start: 0.9256 (m-40) cc_final: 0.8545 (m110) REVERT: D 264 MET cc_start: 0.9063 (mmm) cc_final: 0.8776 (mtp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2173 time to fit residues: 61.8369 Evaluate side-chains 152 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.079392 restraints weight = 29554.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.082062 restraints weight = 17411.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.083957 restraints weight = 11955.433| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13536 Z= 0.347 Angle : 0.706 14.716 18440 Z= 0.353 Chirality : 0.047 0.166 2068 Planarity : 0.006 0.048 2440 Dihedral : 8.282 170.569 2020 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.54 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -1.22 (0.20), residues: 1824 helix: -0.33 (0.19), residues: 728 sheet: -0.18 (0.39), residues: 224 loop : -1.35 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 433 HIS 0.006 0.001 HIS B 348 PHE 0.024 0.002 PHE A 316 TYR 0.012 0.001 TYR A 451 ARG 0.004 0.000 ARG D 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.31 seconds wall clock time: 46 minutes 16.70 seconds (2776.70 seconds total)