Starting phenix.real_space_refine on Tue Sep 24 10:57:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/09_2024/7piv_13454.cif" } resolution = 2.86 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= 0.001 sd= 0.010 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 Ca 1 9.91 5 S 61 5.16 5 C 4909 2.51 5 N 1346 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7814 Number of models: 1 Model: "" Number of chains: 13 Chain: "R" Number of atoms: 1996 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1979 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 260, 1979 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1998 Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" Number of atoms: 1570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 183, 1536 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 183, 1536 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 4 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 1526 Chain: "B" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 2537 Chain: "G" Number of atoms: 421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 414 Chain: "N" Number of atoms: 982 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 976 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 8} Link IDs: {None: 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Conformer: "B" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 67 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Conformer: "B" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" O AHOH A 406 " occ=0.50 pdb=" O BHOH A 406 " occ=0.50 residue: pdb=" O AHOH B 438 " occ=0.50 pdb=" O BHOH B 438 " occ=0.50 Time building chain proxies: 8.46, per 1000 atoms: 1.08 Number of scatterers: 7814 At special positions: 0 Unit cell: (70.72, 96.512, 127.296, 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) Ca 1 19.99 S 61 16.00 O 1497 8.00 N 1346 7.00 C 4909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DPN P 7 " - " HIS P 6 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN P 7 " Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 41.3% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 4.324A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 108 removed outlier: 3.577A pdb=" N PHE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 153 removed outlier: 3.597A pdb=" N ILE R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 191 through 226 removed outlier: 3.512A pdb=" N ILE R 195 " --> pdb=" O SER R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 271 removed outlier: 3.695A pdb=" N THR R 246 " --> pdb=" O LYS R 242 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL R 255 " --> pdb=" O ILE R 251 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.866A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 302 removed outlier: 4.011A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.773A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.760A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.807A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.505A pdb=" N PHE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 377 removed outlier: 3.832A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.548A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.824A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.568A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.805A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ALA A 235 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 234 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.970A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.522A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.771A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 277 through 278 removed outlier: 6.595A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.853A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1102 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: 2.20 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1623 1.34 - 1.46: 1764 1.46 - 1.58: 4389 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 7863 Sorted by residual: bond pdb=" CA GLU R 49 " pdb=" C GLU R 49 " ideal model delta sigma weight residual 1.523 1.614 -0.091 1.37e-02 5.33e+03 4.41e+01 bond pdb=" C SER R 58 " pdb=" N LEU R 59 " ideal model delta sigma weight residual 1.335 1.406 -0.071 1.31e-02 5.83e+03 2.96e+01 bond pdb=" CA SER R 94 " pdb=" CB SER R 94 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.58e-02 4.01e+03 1.97e+01 bond pdb=" N LYS N 87 " pdb=" CA LYS N 87 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N GLU R 49 " pdb=" CA GLU R 49 " ideal model delta sigma weight residual 1.458 1.513 -0.056 1.30e-02 5.92e+03 1.83e+01 ... (remaining 7858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 8376 2.18 - 4.36: 2072 4.36 - 6.54: 223 6.54 - 8.73: 2 8.73 - 10.91: 3 Bond angle restraints: 10676 Sorted by residual: angle pdb=" N HIS R 158 " pdb=" CA AHIS R 158 " pdb=" C HIS R 158 " ideal model delta sigma weight residual 111.75 122.66 -10.91 1.28e+00 6.10e-01 7.26e+01 angle pdb=" N HIS R 158 " pdb=" CA BHIS R 158 " pdb=" C HIS R 158 " ideal model delta sigma weight residual 112.34 122.96 -10.62 1.30e+00 5.92e-01 6.67e+01 angle pdb=" N GLU R 49 " pdb=" CA GLU R 49 " pdb=" C GLU R 49 " ideal model delta sigma weight residual 112.23 103.69 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" C ASN R 120 " pdb=" N ILE R 121 " pdb=" CA ILE R 121 " ideal model delta sigma weight residual 120.56 127.25 -6.69 1.26e+00 6.30e-01 2.82e+01 angle pdb=" O ASN R 120 " pdb=" C ASN R 120 " pdb=" N ILE R 121 " ideal model delta sigma weight residual 122.12 127.64 -5.52 1.06e+00 8.90e-01 2.72e+01 ... (remaining 10671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 4676 35.98 - 71.97: 57 71.97 - 107.95: 5 107.95 - 143.93: 0 143.93 - 179.92: 1 Dihedral angle restraints: 4739 sinusoidal: 1814 harmonic: 2925 Sorted by residual: dihedral pdb=" CD BARG B 314 " pdb=" NE BARG B 314 " pdb=" CZ BARG B 314 " pdb=" NH1BARG B 314 " ideal model delta sinusoidal sigma weight residual 0.00 -179.92 179.92 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" C HIS R 158 " pdb=" N HIS R 158 " pdb=" CA BHIS R 158 " pdb=" CB BHIS R 158 " ideal model delta harmonic sigma weight residual -122.60 -137.69 15.09 0 2.50e+00 1.60e-01 3.64e+01 ... (remaining 4736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 997 0.126 - 0.253: 225 0.253 - 0.379: 2 0.379 - 0.506: 0 0.506 - 0.632: 1 Chirality restraints: 1225 Sorted by residual: chirality pdb=" CA BHIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB BHIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CA AHIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB AHIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ILE R 121 " pdb=" N ILE R 121 " pdb=" C ILE R 121 " pdb=" CB ILE R 121 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1222 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 157 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C TYR R 157 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 157 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS R 158 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 58 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C SER R 58 " 0.043 2.00e-02 2.50e+03 pdb=" O SER R 58 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 59 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 121 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ILE R 121 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 121 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP R 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 805 2.77 - 3.30: 7752 3.30 - 3.83: 11666 3.83 - 4.37: 16725 4.37 - 4.90: 27199 Nonbonded interactions: 64147 Sorted by model distance: nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.234 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.326 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.330 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.344 3.040 ... (remaining 64142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 max=1.00 mean=0.98 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: 5.470 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.013 0.091 7863 Z= 0.857 Angle : 1.706 10.908 10676 Z= 1.285 Chirality : 0.096 0.632 1225 Planarity : 0.002 0.026 1355 Dihedral : 13.139 179.917 2836 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 0.86 % Allowed : 4.40 % Favored : 94.74 % Cbeta Deviations : 0.11 % 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: -2.91 (0.22), residues: 967 helix: -1.68 (0.21), residues: 370 sheet: -1.30 (0.32), residues: 222 loop : -2.42 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 220 HIS 0.004 0.001 HIS R 222 PHE 0.011 0.001 PHE N 68 TYR 0.009 0.001 TYR R 268 ARG 0.003 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 0.873 Fit side-chains REVERT: R 42 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 333 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7186 (mtm-85) REVERT: B 13 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7623 (tm130) REVERT: B 20 ASP cc_start: 0.8395 (m-30) cc_final: 0.8128 (m-30) outliers start: 5 outliers final: 3 residues processed: 155 average time/residue: 1.1220 time to fit residues: 184.8919 Evaluate side-chains 129 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN R 274 ASN B 266 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7863 Z= 0.227 Angle : 0.581 8.796 10676 Z= 0.308 Chirality : 0.042 0.168 1225 Planarity : 0.004 0.049 1355 Dihedral : 7.000 178.700 1108 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.96 % Allowed : 12.47 % Favored : 85.57 % 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: -0.41 (0.25), residues: 967 helix: 1.17 (0.24), residues: 375 sheet: -0.86 (0.32), residues: 235 loop : -1.34 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 220 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.002 PHE R 152 TYR 0.015 0.001 TYR R 287 ARG 0.003 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.911 Fit side-chains REVERT: R 96 SER cc_start: 0.7779 (t) cc_final: 0.7507 (p) REVERT: A 333 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7196 (mtm-85) REVERT: A 342 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7475 (mtm110) REVERT: B 20 ASP cc_start: 0.8342 (m-30) cc_final: 0.8060 (m-30) REVERT: B 188 MET cc_start: 0.8648 (mmm) cc_final: 0.8376 (mmm) REVERT: G 17 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7875 (tp30) outliers start: 15 outliers final: 5 residues processed: 151 average time/residue: 1.2797 time to fit residues: 204.3139 Evaluate side-chains 133 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN A 280 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7863 Z= 0.229 Angle : 0.547 8.490 10676 Z= 0.287 Chirality : 0.041 0.152 1225 Planarity : 0.004 0.041 1355 Dihedral : 6.808 179.526 1104 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.18 % Allowed : 14.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 967 helix: 2.01 (0.26), residues: 374 sheet: -0.54 (0.33), residues: 231 loop : -1.03 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 220 HIS 0.002 0.001 HIS B 183 PHE 0.016 0.002 PHE R 152 TYR 0.016 0.001 TYR R 287 ARG 0.004 0.000 ARG R 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.880 Fit side-chains REVERT: A 333 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: A 342 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7522 (mtm110) REVERT: B 20 ASP cc_start: 0.8334 (m-30) cc_final: 0.8044 (m-30) REVERT: G 17 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7897 (tp30) outliers start: 25 outliers final: 7 residues processed: 139 average time/residue: 1.2469 time to fit residues: 183.3100 Evaluate side-chains 128 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN A 35 GLN B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7863 Z= 0.193 Angle : 0.513 8.212 10676 Z= 0.269 Chirality : 0.040 0.143 1225 Planarity : 0.004 0.038 1355 Dihedral : 6.735 179.424 1104 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.42 % Allowed : 14.79 % Favored : 81.78 % 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: 0.69 (0.27), residues: 967 helix: 2.35 (0.26), residues: 376 sheet: -0.51 (0.33), residues: 233 loop : -0.91 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 220 HIS 0.002 0.001 HIS R 264 PHE 0.013 0.002 PHE R 262 TYR 0.014 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.890 Fit side-chains REVERT: R 270 SER cc_start: 0.8904 (t) cc_final: 0.8616 (p) REVERT: A 330 GLU cc_start: 0.8424 (tp30) cc_final: 0.8200 (tp30) REVERT: A 333 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7144 (mtm-85) REVERT: A 342 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7531 (mtm110) REVERT: B 20 ASP cc_start: 0.8332 (m-30) cc_final: 0.8055 (m-30) outliers start: 27 outliers final: 9 residues processed: 140 average time/residue: 1.2111 time to fit residues: 179.8698 Evaluate side-chains 127 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 ASN R 273 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7863 Z= 0.226 Angle : 0.526 8.185 10676 Z= 0.276 Chirality : 0.041 0.133 1225 Planarity : 0.004 0.039 1355 Dihedral : 6.735 178.951 1104 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.67 % Allowed : 14.67 % Favored : 81.66 % 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: 0.82 (0.28), residues: 967 helix: 2.48 (0.26), residues: 375 sheet: -0.36 (0.34), residues: 231 loop : -0.91 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 220 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.002 PHE B 235 TYR 0.012 0.001 TYR R 287 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.991 Fit side-chains REVERT: R 270 SER cc_start: 0.8904 (t) cc_final: 0.8574 (p) REVERT: A 333 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: A 342 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7535 (mtm110) REVERT: B 20 ASP cc_start: 0.8326 (m-30) cc_final: 0.8060 (m-30) REVERT: B 59 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7615 (m-80) outliers start: 28 outliers final: 9 residues processed: 139 average time/residue: 1.1518 time to fit residues: 170.0481 Evaluate side-chains 127 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 87 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7863 Z= 0.170 Angle : 0.502 7.572 10676 Z= 0.262 Chirality : 0.040 0.134 1225 Planarity : 0.003 0.038 1355 Dihedral : 6.691 179.404 1104 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.18 % Allowed : 16.01 % Favored : 80.81 % 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: 0.96 (0.28), residues: 967 helix: 2.66 (0.26), residues: 375 sheet: -0.40 (0.34), residues: 233 loop : -0.83 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 220 HIS 0.002 0.001 HIS R 264 PHE 0.012 0.001 PHE R 262 TYR 0.023 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.012 Fit side-chains REVERT: R 133 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.7030 (tp) REVERT: R 270 SER cc_start: 0.8919 (t) cc_final: 0.8621 (p) REVERT: A 333 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: A 342 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7511 (mtm110) REVERT: B 20 ASP cc_start: 0.8316 (m-30) cc_final: 0.8061 (m-30) REVERT: B 59 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 101 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: G 17 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7854 (tp30) outliers start: 24 outliers final: 11 residues processed: 143 average time/residue: 1.1415 time to fit residues: 172.9710 Evaluate side-chains 134 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 41 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN R 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7863 Z= 0.166 Angle : 0.501 7.497 10676 Z= 0.261 Chirality : 0.040 0.132 1225 Planarity : 0.003 0.037 1355 Dihedral : 6.664 179.336 1104 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.81 % Allowed : 16.01 % Favored : 81.17 % 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 (0.28), residues: 967 helix: 2.64 (0.26), residues: 381 sheet: -0.33 (0.33), residues: 231 loop : -0.83 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 220 HIS 0.002 0.001 HIS R 264 PHE 0.012 0.001 PHE R 152 TYR 0.019 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.842 Fit side-chains REVERT: R 133 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.7014 (tp) REVERT: R 270 SER cc_start: 0.8925 (t) cc_final: 0.8621 (p) REVERT: A 333 ARG cc_start: 0.7575 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: A 342 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7501 (mtm110) REVERT: B 20 ASP cc_start: 0.8301 (m-30) cc_final: 0.8040 (m-30) REVERT: B 59 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: B 101 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: B 258 ASP cc_start: 0.8329 (t0) cc_final: 0.7927 (t0) REVERT: G 17 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7846 (tp30) outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 1.1634 time to fit residues: 176.5380 Evaluate side-chains 138 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN ** R 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7863 Z= 0.172 Angle : 0.498 7.372 10676 Z= 0.261 Chirality : 0.040 0.131 1225 Planarity : 0.003 0.038 1355 Dihedral : 6.646 179.306 1104 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.69 % Allowed : 16.26 % Favored : 81.05 % 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: 1.05 (0.28), residues: 967 helix: 2.66 (0.26), residues: 381 sheet: -0.28 (0.33), residues: 230 loop : -0.82 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.002 0.001 HIS R 264 PHE 0.012 0.001 PHE R 152 TYR 0.023 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.858 Fit side-chains REVERT: R 133 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7015 (tp) REVERT: R 270 SER cc_start: 0.8939 (t) cc_final: 0.8637 (p) REVERT: A 333 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7236 (mtm-85) REVERT: A 342 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7477 (mtm110) REVERT: B 20 ASP cc_start: 0.8301 (m-30) cc_final: 0.8037 (m-30) REVERT: B 59 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 188 MET cc_start: 0.8628 (mmm) cc_final: 0.8412 (mmp) REVERT: B 258 ASP cc_start: 0.8341 (t0) cc_final: 0.7947 (t0) REVERT: G 17 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7858 (tp30) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 1.1218 time to fit residues: 166.8829 Evaluate side-chains 138 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN R 274 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7863 Z= 0.277 Angle : 0.553 8.010 10676 Z= 0.289 Chirality : 0.042 0.130 1225 Planarity : 0.004 0.040 1355 Dihedral : 6.745 178.018 1104 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.57 % Allowed : 16.63 % Favored : 80.81 % 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: 0.90 (0.27), residues: 967 helix: 2.50 (0.26), residues: 379 sheet: -0.34 (0.33), residues: 231 loop : -0.83 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 220 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE B 235 TYR 0.020 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.885 Fit side-chains REVERT: R 270 SER cc_start: 0.8927 (t) cc_final: 0.8575 (p) REVERT: A 333 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7273 (mtm-85) REVERT: A 342 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7401 (mtm110) REVERT: B 13 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7393 (pt0) REVERT: B 20 ASP cc_start: 0.8345 (m-30) cc_final: 0.8088 (m-30) REVERT: B 59 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: G 17 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7846 (tp30) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 1.1482 time to fit residues: 168.4282 Evaluate side-chains 134 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7863 Z= 0.207 Angle : 0.525 7.565 10676 Z= 0.275 Chirality : 0.041 0.131 1225 Planarity : 0.003 0.039 1355 Dihedral : 6.728 179.029 1104 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.96 % Allowed : 17.36 % Favored : 80.68 % 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: 0.96 (0.27), residues: 967 helix: 2.51 (0.26), residues: 382 sheet: -0.31 (0.33), residues: 231 loop : -0.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 220 HIS 0.002 0.001 HIS R 264 PHE 0.014 0.002 PHE R 152 TYR 0.027 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.875 Fit side-chains REVERT: R 270 SER cc_start: 0.8913 (t) cc_final: 0.8564 (p) REVERT: A 333 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7253 (mtm-85) REVERT: A 342 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7383 (mtm110) REVERT: B 13 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7346 (pt0) REVERT: B 20 ASP cc_start: 0.8347 (m-30) cc_final: 0.8088 (m-30) REVERT: B 59 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: B 188 MET cc_start: 0.8633 (mmm) cc_final: 0.8429 (mmp) REVERT: G 17 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7835 (tp30) outliers start: 14 outliers final: 9 residues processed: 136 average time/residue: 1.1364 time to fit residues: 164.0660 Evaluate side-chains 130 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103598 restraints weight = 51194.391| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.73 r_work: 0.3086 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7863 Z= 0.204 Angle : 0.524 7.520 10676 Z= 0.274 Chirality : 0.040 0.129 1225 Planarity : 0.003 0.040 1355 Dihedral : 6.706 178.979 1104 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.20 % Allowed : 17.24 % Favored : 80.56 % 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: 0.99 (0.27), residues: 967 helix: 2.52 (0.26), residues: 382 sheet: -0.31 (0.33), residues: 231 loop : -0.74 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 263 HIS 0.002 0.001 HIS B 142 PHE 0.014 0.002 PHE R 152 TYR 0.017 0.001 TYR R 287 ARG 0.003 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.73 seconds wall clock time: 60 minutes 19.24 seconds (3619.24 seconds total)