Starting phenix.real_space_refine on Tue Feb 13 21:29:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/02_2024/7piv_13454_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/02_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_13454/02_2024/7piv_13454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/02_2024/7piv_13454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/02_2024/7piv_13454_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piv_13454/02_2024/7piv_13454_updated.pdb" } 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 Residue "R GLU 49": "OE1" <-> "OE2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R ARG 305": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7814 Number of models: 1 Model: "" Number of chains: 12 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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 114 Classifications: {'peptide': 13} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} 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: "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: 9.11, per 1000 atoms: 1.17 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 22 helices and 10 sheets defined 37.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'R' and resid 48 through 70 removed outlier: 4.065A pdb=" N VAL R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 107 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 152 removed outlier: 3.597A pdb=" N ILE R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 186 Processing helix chain 'R' and resid 192 through 227 removed outlier: 3.808A pdb=" N ALA R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 270 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 275 through 301 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) removed outlier: 4.417A pdb=" N HIS R 283 " --> pdb=" O CYS R 279 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN R 285 " --> pdb=" O MET R 281 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) 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 307 through 315 Processing helix chain 'A' and resid 14 through 39 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 220 through 223 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 323 through 337 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) Processing helix chain 'A' and resid 357 through 376 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 25 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 30 through 36 removed outlier: 4.743A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.568A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 345 through 349 removed outlier: 7.171A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 229 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 44 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 233 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.219A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.969A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) 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= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.112A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.877A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.188A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.811A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 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) 358 hydrogen bonds defined for protein. 1030 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: 2.75 Time building geometry restraints manager: 3.80 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: 1765 1.46 - 1.58: 4389 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 7864 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 7859 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.16: 181 107.16 - 114.00: 4443 114.00 - 120.84: 3465 120.84 - 127.68: 2536 127.68 - 134.52: 54 Bond angle restraints: 10679 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 10674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 4674 35.98 - 71.97: 57 71.97 - 107.95: 5 107.95 - 143.93: 0 143.93 - 179.92: 1 Dihedral angle restraints: 4737 sinusoidal: 1812 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 4734 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: 808 2.77 - 3.30: 7780 3.30 - 3.83: 11694 3.83 - 4.37: 16786 4.37 - 4.90: 27198 Nonbonded interactions: 64266 Sorted by model distance: nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.234 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.326 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.330 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.344 2.440 ... (remaining 64261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.300 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: 0.000 Extract box with map and model: 6.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- 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 7864 Z= 0.862 Angle : 1.706 10.908 10679 Z= 1.285 Chirality : 0.096 0.632 1225 Planarity : 0.002 0.026 1356 Dihedral : 13.137 179.917 2837 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 : 1.071 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: 1.1631 time to fit residues: 191.6536 Evaluate side-chains 129 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7864 Z= 0.224 Angle : 0.569 9.471 10679 Z= 0.301 Chirality : 0.041 0.170 1225 Planarity : 0.004 0.049 1356 Dihedral : 6.960 178.837 1109 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.44 % Allowed : 12.22 % Favored : 85.33 % 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: -0.44 (0.26), residues: 967 helix: 1.15 (0.24), residues: 373 sheet: -0.95 (0.32), residues: 240 loop : -1.29 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.002 PHE R 152 TYR 0.028 0.001 TYR R 287 ARG 0.002 0.000 ARG G 13 *********************** 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 156 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.345 Fit side-chains REVERT: A 333 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7160 (mtm-85) REVERT: A 342 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7464 (mtm110) REVERT: A 372 MET cc_start: 0.7885 (tmm) cc_final: 0.7669 (ttt) REVERT: B 20 ASP cc_start: 0.8271 (m-30) cc_final: 0.7984 (m-30) REVERT: G 17 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7874 (tp30) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 1.2544 time to fit residues: 194.7314 Evaluate side-chains 128 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 R residue 189 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7864 Z= 0.210 Angle : 0.524 8.960 10679 Z= 0.273 Chirality : 0.040 0.152 1225 Planarity : 0.004 0.039 1356 Dihedral : 6.762 179.573 1105 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.57 % Allowed : 14.55 % Favored : 82.89 % 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: 0.33 (0.27), residues: 967 helix: 2.01 (0.26), residues: 376 sheet: -0.69 (0.34), residues: 233 loop : -1.06 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.015 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 146 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.869 Fit side-chains REVERT: A 251 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5932 (ttp80) REVERT: A 333 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7127 (mtm-85) REVERT: A 342 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7505 (mtm110) REVERT: B 20 ASP cc_start: 0.8277 (m-30) cc_final: 0.8003 (m-30) REVERT: B 23 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7650 (tppt) REVERT: G 17 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7886 (tp30) REVERT: G 28 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8674 (pp) outliers start: 20 outliers final: 5 residues processed: 136 average time/residue: 1.3718 time to fit residues: 196.4963 Evaluate side-chains 125 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7864 Z= 0.207 Angle : 0.512 8.837 10679 Z= 0.267 Chirality : 0.040 0.140 1225 Planarity : 0.004 0.038 1356 Dihedral : 6.718 179.341 1105 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.79 % Allowed : 14.79 % Favored : 81.42 % 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: 0.61 (0.27), residues: 967 helix: 2.25 (0.26), residues: 376 sheet: -0.57 (0.33), residues: 232 loop : -0.89 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.014 0.002 PHE R 152 TYR 0.021 0.001 TYR R 287 ARG 0.004 0.000 ARG R 225 *********************** 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 155 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.846 Fit side-chains REVERT: A 251 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6035 (ttp80) REVERT: A 333 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7148 (mtm-85) REVERT: A 342 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7512 (mtm110) REVERT: B 20 ASP cc_start: 0.8251 (m-30) cc_final: 0.7970 (m-30) REVERT: B 23 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7591 (tppp) REVERT: B 312 ASP cc_start: 0.7755 (m-30) cc_final: 0.7533 (m-30) REVERT: B 333 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7276 (m-30) outliers start: 29 outliers final: 10 residues processed: 140 average time/residue: 1.1800 time to fit residues: 175.1925 Evaluate side-chains 131 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain R residue 189 ASP Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 333 ASP 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: 95 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7864 Z= 0.243 Angle : 0.524 8.896 10679 Z= 0.272 Chirality : 0.041 0.129 1225 Planarity : 0.004 0.039 1356 Dihedral : 6.721 178.933 1105 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.18 % Allowed : 15.65 % 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: 0.72 (0.28), residues: 967 helix: 2.35 (0.26), residues: 376 sheet: -0.63 (0.34), residues: 235 loop : -0.73 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.002 PHE R 152 TYR 0.023 0.001 TYR R 287 ARG 0.003 0.000 ARG R 225 *********************** 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: 24 poor density : 126 time to evaluate : 0.854 Fit side-chains REVERT: R 270 SER cc_start: 0.8902 (t) cc_final: 0.8576 (p) REVERT: A 45 LEU cc_start: 0.8537 (tp) cc_final: 0.8298 (tt) REVERT: A 251 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6030 (ttp80) REVERT: A 342 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7538 (mtm110) REVERT: B 20 ASP cc_start: 0.8270 (m-30) cc_final: 0.8001 (m-30) REVERT: B 23 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7543 (tppp) REVERT: G 28 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8718 (pp) outliers start: 24 outliers final: 12 residues processed: 140 average time/residue: 1.1840 time to fit residues: 176.4084 Evaluate side-chains 137 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 189 ASP Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 42 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 A 35 GLN B B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7864 Z= 0.153 Angle : 0.484 7.901 10679 Z= 0.252 Chirality : 0.039 0.130 1225 Planarity : 0.003 0.036 1356 Dihedral : 6.654 179.734 1105 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.30 % Allowed : 15.89 % 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: 0.84 (0.28), residues: 967 helix: 2.49 (0.26), residues: 376 sheet: -0.55 (0.33), residues: 233 loop : -0.74 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.012 0.001 PHE R 262 TYR 0.026 0.001 TYR R 287 ARG 0.003 0.000 ARG R 225 *********************** 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 162 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.953 Fit side-chains REVERT: R 84 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7613 (m) REVERT: R 270 SER cc_start: 0.8894 (t) cc_final: 0.8570 (p) REVERT: A 251 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6080 (ttp80) REVERT: A 333 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: A 342 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7509 (mtm110) REVERT: B 20 ASP cc_start: 0.8269 (m-30) cc_final: 0.8014 (m-30) REVERT: B 23 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7425 (tppp) REVERT: G 17 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7823 (tp30) REVERT: G 28 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8675 (pp) REVERT: N 83 MET cc_start: 0.9158 (mtp) cc_final: 0.8956 (mtp) outliers start: 25 outliers final: 13 residues processed: 152 average time/residue: 1.1779 time to fit residues: 189.9261 Evaluate side-chains 146 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 189 ASP Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7864 Z= 0.174 Angle : 0.491 8.091 10679 Z= 0.256 Chirality : 0.040 0.126 1225 Planarity : 0.003 0.036 1356 Dihedral : 6.645 179.389 1105 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.30 % Allowed : 16.01 % 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: 0.90 (0.28), residues: 967 helix: 2.47 (0.26), residues: 378 sheet: -0.50 (0.33), residues: 232 loop : -0.66 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.003 0.001 HIS R 264 PHE 0.013 0.001 PHE R 152 TYR 0.016 0.001 TYR R 287 ARG 0.003 0.000 ARG R 225 *********************** 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 158 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.908 Fit side-chains REVERT: R 84 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7645 (m) REVERT: R 270 SER cc_start: 0.8924 (t) cc_final: 0.8630 (p) REVERT: A 45 LEU cc_start: 0.8546 (tp) cc_final: 0.8291 (tt) REVERT: A 251 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6203 (ttp80) REVERT: A 333 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.7147 (mtm-85) REVERT: A 342 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7484 (mtm110) REVERT: B 20 ASP cc_start: 0.8268 (m-30) cc_final: 0.8011 (m-30) REVERT: B 23 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7404 (tppp) REVERT: G 17 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7828 (tp30) REVERT: G 28 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8698 (pp) outliers start: 25 outliers final: 11 residues processed: 147 average time/residue: 1.2147 time to fit residues: 189.0194 Evaluate side-chains 147 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7864 Z= 0.215 Angle : 0.515 8.254 10679 Z= 0.268 Chirality : 0.040 0.136 1225 Planarity : 0.003 0.037 1356 Dihedral : 6.661 179.155 1105 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.06 % Allowed : 16.99 % Favored : 79.95 % 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: 0.91 (0.28), residues: 967 helix: 2.42 (0.26), residues: 378 sheet: -0.42 (0.34), residues: 231 loop : -0.63 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.015 0.002 PHE R 152 TYR 0.022 0.001 TYR R 287 ARG 0.003 0.000 ARG R 225 *********************** 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 151 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.790 Fit side-chains REVERT: R 84 CYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7626 (m) REVERT: R 270 SER cc_start: 0.8933 (t) cc_final: 0.8637 (p) REVERT: R 273 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: A 251 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6229 (ttp80) REVERT: A 333 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: A 342 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7466 (mtm110) REVERT: B 20 ASP cc_start: 0.8286 (m-30) cc_final: 0.8025 (m-30) REVERT: B 23 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7420 (tppp) REVERT: G 17 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7806 (tp30) REVERT: G 28 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8718 (pp) outliers start: 23 outliers final: 15 residues processed: 143 average time/residue: 1.1936 time to fit residues: 180.8077 Evaluate side-chains 145 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP 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 B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7864 Z= 0.219 Angle : 0.516 8.237 10679 Z= 0.268 Chirality : 0.040 0.138 1225 Planarity : 0.003 0.038 1356 Dihedral : 6.656 179.153 1105 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 17.36 % Favored : 79.83 % 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: 0.95 (0.28), residues: 967 helix: 2.46 (0.26), residues: 375 sheet: -0.38 (0.34), residues: 231 loop : -0.61 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.015 0.002 PHE R 152 TYR 0.010 0.001 TYR R 287 ARG 0.003 0.000 ARG R 225 *********************** 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 146 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.172 Fit side-chains REVERT: R 84 CYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7614 (m) REVERT: R 270 SER cc_start: 0.8944 (t) cc_final: 0.8627 (p) REVERT: A 251 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6224 (ttp80) REVERT: A 333 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7085 (mtm-85) REVERT: A 342 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7475 (mtm110) REVERT: B 20 ASP cc_start: 0.8307 (m-30) cc_final: 0.8050 (m-30) REVERT: B 23 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7426 (tppp) REVERT: G 17 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7810 (tp30) REVERT: G 28 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8729 (pp) outliers start: 21 outliers final: 15 residues processed: 139 average time/residue: 1.1605 time to fit residues: 171.3758 Evaluate side-chains 141 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP 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 B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 0.0570 chunk 87 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 273 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 7864 Z= 0.159 Angle : 0.493 7.610 10679 Z= 0.256 Chirality : 0.040 0.135 1225 Planarity : 0.003 0.037 1356 Dihedral : 6.646 179.712 1105 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.93 % Allowed : 17.24 % Favored : 79.83 % 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: 1.02 (0.28), residues: 967 helix: 2.54 (0.26), residues: 375 sheet: -0.38 (0.33), residues: 231 loop : -0.57 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.012 0.001 PHE R 152 TYR 0.025 0.001 TYR R 287 ARG 0.001 0.000 ARG A 371 ********************** 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 155 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.843 Fit side-chains REVERT: R 84 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7550 (m) REVERT: R 270 SER cc_start: 0.8934 (t) cc_final: 0.8630 (p) REVERT: R 273 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: A 333 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7137 (mtm-85) REVERT: A 342 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7464 (mtm110) REVERT: B 20 ASP cc_start: 0.8302 (m-30) cc_final: 0.8043 (m-30) REVERT: B 23 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7383 (tppp) REVERT: G 17 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7808 (tp30) REVERT: G 28 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8697 (pp) outliers start: 22 outliers final: 15 residues processed: 147 average time/residue: 1.1636 time to fit residues: 182.4738 Evaluate side-chains 145 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 180 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP 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 B residue 333 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** 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 = 0.3698 r_free = 0.3698 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104854 restraints weight = 51139.054| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.75 r_work: 0.3097 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 7864 Z= 0.286 Angle : 1.033 59.178 10679 Z= 0.587 Chirality : 0.041 0.350 1225 Planarity : 0.003 0.037 1356 Dihedral : 6.651 179.703 1105 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.69 % Allowed : 17.60 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 967 helix: 2.54 (0.26), residues: 375 sheet: -0.37 (0.33), residues: 231 loop : -0.57 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 264 PHE 0.012 0.001 PHE R 152 TYR 0.019 0.001 TYR R 287 ARG 0.001 0.000 ARG N 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.20 seconds wall clock time: 63 minutes 41.54 seconds (3821.54 seconds total)