Starting phenix.real_space_refine on Tue Sep 24 10:23:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/09_2024/7piu_13453.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 62 5.16 5 C 4911 2.51 5 N 1350 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7788 Number of models: 1 Model: "" Number of chains: 14 Chain: "R" Number of atoms: 2005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1988 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 259, 1988 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2010 Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 1581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 189, 1573 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 189, 1573 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 5 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1594 Chain: "B" Number of atoms: 2629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2561 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 337, 2561 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 2529 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: 986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 976 Chain: "R" Number of atoms: 6 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Conformer: "B" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Conformer: "B" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 51 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Conformer: "B" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" O AHOH R 504 " occ=0.50 pdb=" O BHOH R 504 " occ=0.50 residue: pdb=" O AHOH A 414 " occ=0.50 pdb=" O BHOH A 414 " occ=0.50 residue: pdb=" O AHOH B 405 " occ=0.50 pdb=" O BHOH B 405 " occ=0.50 Time building chain proxies: 8.39, per 1000 atoms: 1.08 Number of scatterers: 7788 At special positions: 0 Unit cell: (73.216, 97.344, 128.96, 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 62 16.00 O 1464 8.00 N 1350 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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 P 2 " - pdb=" SG CYS P 8 " distance=2.04 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=2.03 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 " DAL P 3 " - " CYS P 2 " " DPN P 5 " - " HIS P 4 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 3 " pdb=" CB DPN P 5 " Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 41.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.997A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 54 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 76 Processing helix chain 'R' and resid 77 through 107 removed outlier: 3.734A pdb=" N PHE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE R 83 " --> pdb=" O MET R 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 153 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 227 removed outlier: 3.703A pdb=" N ARG R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 271 removed outlier: 3.815A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.773A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 302 removed outlier: 3.624A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.596A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.654A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.539A pdb=" N PHE A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 removed outlier: 4.020A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 377 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.671A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.982A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 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 194 through 199 removed outlier: 3.744A pdb=" N PHE A 194 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS A 41 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 208 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 43 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA A 235 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.606A 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: 6.738A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.760A 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: 6.372A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.840A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A 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: 7.019A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.219A 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: 6.692A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.688A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.810A 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 removed outlier: 3.624A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.072A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1109 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: 2.13 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1248 1.32 - 1.44: 2129 1.44 - 1.57: 4396 1.57 - 1.69: 1 1.69 - 1.82: 86 Bond restraints: 7860 Sorted by residual: bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.460 1.496 -0.036 8.60e-03 1.35e+04 1.72e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.29e+01 bond pdb=" C GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 1.522 1.570 -0.047 1.36e-02 5.41e+03 1.20e+01 bond pdb=" N GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.19e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.14e+01 ... (remaining 7855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8446 2.20 - 4.39: 2006 4.39 - 6.59: 206 6.59 - 8.78: 8 8.78 - 10.98: 4 Bond angle restraints: 10670 Sorted by residual: angle pdb=" O GLU R 100 " pdb=" C GLU R 100 " pdb=" CA BGLU R 100 " ideal model delta sigma weight residual 120.10 131.08 -10.98 1.13e+00 7.83e-01 9.44e+01 angle pdb=" O GLU R 100 " pdb=" C GLU R 100 " pdb=" CA AGLU R 100 " ideal model delta sigma weight residual 119.31 129.07 -9.76 1.24e+00 6.50e-01 6.20e+01 angle pdb=" N GLU R 100 " pdb=" CA AGLU R 100 " pdb=" C GLU R 100 " ideal model delta sigma weight residual 112.89 120.76 -7.87 1.24e+00 6.50e-01 4.03e+01 angle pdb=" N ARG B 46 " pdb=" CA BARG B 46 " pdb=" C ARG B 46 " ideal model delta sigma weight residual 109.72 119.65 -9.93 1.60e+00 3.91e-01 3.85e+01 angle pdb=" O ARG B 46 " pdb=" C ARG B 46 " pdb=" CA BARG B 46 " ideal model delta sigma weight residual 121.11 128.10 -6.99 1.13e+00 7.83e-01 3.82e+01 ... (remaining 10665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 4643 35.97 - 71.95: 87 71.95 - 107.92: 4 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 4735 sinusoidal: 1822 harmonic: 2913 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 -179.87 179.87 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 4732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 502 0.069 - 0.137: 559 0.137 - 0.206: 163 0.206 - 0.274: 3 0.274 - 0.343: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA AGLU R 100 " pdb=" N GLU R 100 " pdb=" C GLU R 100 " pdb=" CB AGLU R 100 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+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 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA MET B 45 " pdb=" N MET B 45 " pdb=" C MET B 45 " pdb=" CB MET B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1227 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 44 " -0.054 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" O GLN B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CA BGLN B 44 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 45 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 44 " -0.052 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" O GLN B 44 " 0.019 2.00e-02 2.50e+03 pdb=" CA AGLN B 44 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 45 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 46 " 0.050 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" O ARG B 46 " -0.020 2.00e-02 2.50e+03 pdb=" CA BARG B 46 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 47 " -0.016 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 911 2.78 - 3.31: 7470 3.31 - 3.84: 12114 3.84 - 4.37: 17240 4.37 - 4.90: 27354 Nonbonded interactions: 65089 Sorted by model distance: nonbonded pdb=" O VAL R 119 " pdb=" OD1 ASN R 123 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP G 48 " pdb=" O HOH G 101 " model vdw 2.280 3.040 nonbonded pdb=" O GLY B 64 " pdb=" O HOH B 401 " model vdw 2.335 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.343 3.040 ... (remaining 65084 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.710 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: 0.000 Load rotamer database and sin/cos tables:16.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 0.047 7860 Z= 0.861 Angle : 1.707 10.981 10670 Z= 1.283 Chirality : 0.094 0.343 1230 Planarity : 0.003 0.031 1351 Dihedral : 14.839 179.868 2832 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 0.97 % Allowed : 6.21 % Favored : 92.81 % 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: -2.07 (0.23), residues: 963 helix: -1.60 (0.21), residues: 373 sheet: -0.51 (0.32), residues: 211 loop : -1.41 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 220 HIS 0.004 0.001 HIS A 343 PHE 0.016 0.001 PHE A 194 TYR 0.010 0.001 TYR B 85 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 0.841 Fit side-chains REVERT: A 20 ARG cc_start: 0.6912 (mtp-110) cc_final: 0.6555 (mtm-85) REVERT: B 6 GLN cc_start: 0.6842 (tt0) cc_final: 0.5663 (pm20) REVERT: B 96 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.7476 (mtm-85) REVERT: B 186 ASP cc_start: 0.7875 (m-30) cc_final: 0.7625 (m-30) REVERT: N 3 GLN cc_start: 0.8169 (tt0) cc_final: 0.7900 (tt0) REVERT: N 99 CYS cc_start: 0.7851 (m) cc_final: 0.7508 (m) outliers start: 7 outliers final: 4 residues processed: 187 average time/residue: 1.3019 time to fit residues: 257.2673 Evaluate side-chains 145 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 245 ILE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 ASN A 253 GLN A 357 ASN B 266 HIS G 18 GLN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7860 Z= 0.183 Angle : 0.517 4.399 10670 Z= 0.291 Chirality : 0.041 0.135 1230 Planarity : 0.004 0.028 1351 Dihedral : 7.084 179.409 1104 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.56 % Allowed : 12.42 % Favored : 85.02 % 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: 0.54 (0.26), residues: 963 helix: 1.59 (0.25), residues: 380 sheet: 0.14 (0.31), residues: 222 loop : -0.78 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 PHE 0.013 0.002 PHE R 152 TYR 0.011 0.001 TYR R 157 ARG 0.006 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.824 Fit side-chains REVERT: R 91 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7298 (tmm) REVERT: A 20 ARG cc_start: 0.6851 (mtp-110) cc_final: 0.6421 (mtm-85) REVERT: A 254 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: B 6 GLN cc_start: 0.6937 (tt0) cc_final: 0.5726 (pm20) REVERT: B 59 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 186 ASP cc_start: 0.8131 (m-30) cc_final: 0.7914 (m-30) REVERT: B 217 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (pmt) REVERT: B 219 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7725 (mtp85) REVERT: G 21 MET cc_start: 0.7905 (tpp) cc_final: 0.7414 (tmt) REVERT: N 3 GLN cc_start: 0.8006 (tt0) cc_final: 0.7765 (tt0) REVERT: N 99 CYS cc_start: 0.7825 (m) cc_final: 0.7518 (m) outliers start: 20 outliers final: 5 residues processed: 157 average time/residue: 1.2649 time to fit residues: 209.7267 Evaluate side-chains 136 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 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: A 280 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7860 Z= 0.193 Angle : 0.506 8.829 10670 Z= 0.279 Chirality : 0.041 0.153 1230 Planarity : 0.004 0.035 1351 Dihedral : 6.813 178.422 1098 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.05 % Allowed : 12.91 % Favored : 84.04 % 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: 1.30 (0.27), residues: 963 helix: 2.53 (0.26), residues: 380 sheet: 0.34 (0.32), residues: 222 loop : -0.60 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS A 343 PHE 0.017 0.002 PHE R 152 TYR 0.016 0.001 TYR N 60 ARG 0.013 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.854 Fit side-chains REVERT: R 91 MET cc_start: 0.7533 (tmm) cc_final: 0.7304 (tmm) REVERT: A 20 ARG cc_start: 0.6810 (mtp-110) cc_final: 0.6394 (mtm-85) REVERT: A 25 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7747 (mptp) REVERT: A 376 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: B 6 GLN cc_start: 0.6985 (tt0) cc_final: 0.5874 (pm20) REVERT: B 59 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8351 (t80) REVERT: B 186 ASP cc_start: 0.8181 (m-30) cc_final: 0.7980 (m-30) REVERT: B 217 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7864 (pmt) REVERT: B 219 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7722 (mtp85) REVERT: G 21 MET cc_start: 0.7963 (tpp) cc_final: 0.7542 (tmt) REVERT: N 3 GLN cc_start: 0.8035 (tt0) cc_final: 0.7780 (tt0) REVERT: N 89 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: N 99 CYS cc_start: 0.7828 (m) cc_final: 0.7504 (m) outliers start: 24 outliers final: 8 residues processed: 148 average time/residue: 1.2881 time to fit residues: 200.9012 Evaluate side-chains 143 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7860 Z= 0.209 Angle : 0.498 7.976 10670 Z= 0.274 Chirality : 0.041 0.145 1230 Planarity : 0.004 0.039 1351 Dihedral : 6.822 178.212 1097 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 3.41 % Allowed : 12.91 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 963 helix: 2.76 (0.26), residues: 380 sheet: 0.47 (0.32), residues: 227 loop : -0.44 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 220 HIS 0.006 0.001 HIS A 343 PHE 0.015 0.002 PHE R 152 TYR 0.017 0.001 TYR N 60 ARG 0.005 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.893 Fit side-chains REVERT: A 20 ARG cc_start: 0.6832 (mtp-110) cc_final: 0.6395 (mtm-85) REVERT: A 25 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (mptp) REVERT: A 376 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: B 6 GLN cc_start: 0.6987 (tt0) cc_final: 0.5873 (pm20) REVERT: B 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8300 (t80) REVERT: B 186 ASP cc_start: 0.8190 (m-30) cc_final: 0.7866 (m-30) REVERT: B 217 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7919 (pmt) REVERT: B 219 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7704 (mtp85) REVERT: G 21 MET cc_start: 0.7935 (tpp) cc_final: 0.7496 (tmt) REVERT: G 22 GLU cc_start: 0.8096 (pt0) cc_final: 0.7705 (tt0) REVERT: G 28 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8221 (pp) REVERT: N 3 GLN cc_start: 0.8055 (tt0) cc_final: 0.7790 (tt0) REVERT: N 99 CYS cc_start: 0.7862 (m) cc_final: 0.7532 (m) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 1.3080 time to fit residues: 192.8780 Evaluate side-chains 146 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.0000 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7860 Z= 0.215 Angle : 0.501 7.718 10670 Z= 0.275 Chirality : 0.041 0.138 1230 Planarity : 0.004 0.040 1351 Dihedral : 6.809 178.047 1097 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 3.29 % Allowed : 14.25 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 963 helix: 2.86 (0.26), residues: 380 sheet: 0.47 (0.32), residues: 232 loop : -0.40 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS A 343 PHE 0.014 0.002 PHE R 152 TYR 0.019 0.001 TYR N 60 ARG 0.013 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.869 Fit side-chains REVERT: A 20 ARG cc_start: 0.6839 (mtp-110) cc_final: 0.6399 (mtm-85) REVERT: A 25 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7716 (mptp) REVERT: A 376 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: B 6 GLN cc_start: 0.7130 (tt0) cc_final: 0.6071 (pm20) REVERT: B 59 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8326 (t80) REVERT: B 186 ASP cc_start: 0.8196 (m-30) cc_final: 0.7993 (m-30) REVERT: B 217 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7950 (pmt) REVERT: G 21 MET cc_start: 0.7946 (tpp) cc_final: 0.7476 (tmt) REVERT: G 22 GLU cc_start: 0.8054 (pt0) cc_final: 0.7779 (tt0) REVERT: G 28 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8213 (pp) REVERT: N 3 GLN cc_start: 0.8052 (tt0) cc_final: 0.7779 (tt0) REVERT: N 99 CYS cc_start: 0.7864 (m) cc_final: 0.7550 (m) outliers start: 25 outliers final: 13 residues processed: 145 average time/residue: 1.3444 time to fit residues: 205.1643 Evaluate side-chains 145 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN G 59 ASN N 39 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7860 Z= 0.174 Angle : 0.475 7.466 10670 Z= 0.261 Chirality : 0.040 0.135 1230 Planarity : 0.004 0.044 1351 Dihedral : 6.743 178.864 1097 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.80 % Allowed : 14.98 % Favored : 82.22 % 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: 1.78 (0.27), residues: 963 helix: 3.03 (0.26), residues: 380 sheet: 0.47 (0.32), residues: 227 loop : -0.40 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 PHE 0.012 0.002 PHE R 262 TYR 0.018 0.001 TYR N 60 ARG 0.006 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.795 Fit side-chains REVERT: R 292 MET cc_start: 0.8140 (mtm) cc_final: 0.7938 (mtt) REVERT: A 20 ARG cc_start: 0.6822 (mtp-110) cc_final: 0.6405 (mtm-85) REVERT: A 25 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7767 (mptp) REVERT: A 376 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: B 6 GLN cc_start: 0.7151 (tt0) cc_final: 0.6108 (pm20) REVERT: B 59 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8324 (t80) REVERT: B 217 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7930 (pmt) REVERT: G 21 MET cc_start: 0.7934 (tpp) cc_final: 0.7471 (tmt) REVERT: G 22 GLU cc_start: 0.8049 (pt0) cc_final: 0.7847 (tt0) REVERT: G 28 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8219 (pp) REVERT: N 3 GLN cc_start: 0.8039 (tt0) cc_final: 0.7766 (tt0) REVERT: N 99 CYS cc_start: 0.7866 (m) cc_final: 0.7553 (m) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 1.3007 time to fit residues: 191.9811 Evaluate side-chains 148 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7860 Z= 0.194 Angle : 0.485 7.331 10670 Z= 0.266 Chirality : 0.041 0.135 1230 Planarity : 0.004 0.045 1351 Dihedral : 6.751 178.402 1097 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 15.23 % Favored : 81.36 % 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: 1.79 (0.27), residues: 963 helix: 3.05 (0.25), residues: 380 sheet: 0.38 (0.32), residues: 225 loop : -0.34 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 PHE 0.023 0.002 PHE R 45 TYR 0.008 0.001 TYR A 344 ARG 0.013 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.865 Fit side-chains REVERT: A 20 ARG cc_start: 0.6807 (mtp-110) cc_final: 0.6376 (mtm-85) REVERT: A 25 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7737 (mptp) REVERT: A 266 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7690 (ttt90) REVERT: A 376 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: B 6 GLN cc_start: 0.7132 (tt0) cc_final: 0.6087 (pm20) REVERT: B 59 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8324 (t80) REVERT: B 217 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8191 (pmt) REVERT: G 21 MET cc_start: 0.7950 (tpp) cc_final: 0.7497 (tmt) REVERT: G 28 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8202 (pp) REVERT: N 3 GLN cc_start: 0.8046 (tt0) cc_final: 0.7769 (tt0) REVERT: N 99 CYS cc_start: 0.7868 (m) cc_final: 0.7560 (m) outliers start: 26 outliers final: 13 residues processed: 140 average time/residue: 1.3176 time to fit residues: 194.4964 Evaluate side-chains 149 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7860 Z= 0.168 Angle : 0.473 7.200 10670 Z= 0.260 Chirality : 0.040 0.134 1230 Planarity : 0.003 0.037 1351 Dihedral : 6.700 178.851 1097 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.92 % Allowed : 15.71 % Favored : 81.36 % 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: 1.82 (0.27), residues: 963 helix: 3.11 (0.26), residues: 381 sheet: 0.39 (0.32), residues: 220 loop : -0.35 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 343 PHE 0.012 0.002 PHE R 262 TYR 0.019 0.001 TYR N 60 ARG 0.007 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 0.780 Fit side-chains REVERT: R 224 LYS cc_start: 0.8614 (tppt) cc_final: 0.8386 (mttp) REVERT: A 20 ARG cc_start: 0.6856 (mtp-110) cc_final: 0.6428 (mtm-85) REVERT: A 25 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7718 (mptp) REVERT: A 266 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7691 (ttt90) REVERT: A 376 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 6 GLN cc_start: 0.7157 (tt0) cc_final: 0.6116 (pm20) REVERT: B 59 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8234 (t80) REVERT: B 217 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8202 (pmt) REVERT: G 21 MET cc_start: 0.7903 (tpp) cc_final: 0.7510 (tmt) REVERT: G 28 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8198 (pp) REVERT: N 3 GLN cc_start: 0.8040 (tt0) cc_final: 0.7762 (tt0) REVERT: N 99 CYS cc_start: 0.7854 (m) cc_final: 0.7547 (m) outliers start: 22 outliers final: 10 residues processed: 144 average time/residue: 1.3119 time to fit residues: 199.1239 Evaluate side-chains 148 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 123 ASN R 159 ASN A 280 GLN B 237 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7860 Z= 0.166 Angle : 0.473 7.133 10670 Z= 0.260 Chirality : 0.040 0.134 1230 Planarity : 0.004 0.057 1351 Dihedral : 6.684 178.805 1097 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 16.69 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 963 helix: 3.12 (0.25), residues: 381 sheet: 0.37 (0.32), residues: 220 loop : -0.34 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 343 PHE 0.026 0.002 PHE R 45 TYR 0.020 0.001 TYR N 60 ARG 0.014 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.830 Fit side-chains REVERT: A 15 GLU cc_start: 0.7726 (tp30) cc_final: 0.7402 (mm-30) REVERT: A 20 ARG cc_start: 0.6852 (mtp-110) cc_final: 0.6427 (mtm-85) REVERT: A 25 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7712 (mptp) REVERT: A 266 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7687 (ttt90) REVERT: A 376 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: B 6 GLN cc_start: 0.7151 (tt0) cc_final: 0.6106 (pm20) REVERT: B 59 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8302 (t80) REVERT: B 217 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8202 (pmt) REVERT: G 21 MET cc_start: 0.7941 (tpp) cc_final: 0.7532 (tmt) REVERT: G 28 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8198 (pp) REVERT: N 3 GLN cc_start: 0.8033 (tt0) cc_final: 0.7755 (tt0) REVERT: N 99 CYS cc_start: 0.7856 (m) cc_final: 0.7601 (m) outliers start: 17 outliers final: 9 residues processed: 140 average time/residue: 1.2961 time to fit residues: 191.5062 Evaluate side-chains 147 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 0.0030 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 280 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7860 Z= 0.121 Angle : 0.444 7.019 10670 Z= 0.244 Chirality : 0.039 0.134 1230 Planarity : 0.003 0.035 1351 Dihedral : 6.583 179.916 1097 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 17.30 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.27), residues: 963 helix: 3.24 (0.26), residues: 382 sheet: 0.49 (0.32), residues: 231 loop : -0.34 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 343 PHE 0.012 0.001 PHE R 262 TYR 0.022 0.001 TYR N 60 ARG 0.009 0.000 ARG R 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.800 Fit side-chains REVERT: R 224 LYS cc_start: 0.8603 (tppt) cc_final: 0.8369 (mttp) REVERT: A 15 GLU cc_start: 0.7677 (tp30) cc_final: 0.7460 (mm-30) REVERT: A 20 ARG cc_start: 0.6829 (mtp-110) cc_final: 0.6431 (mtm-85) REVERT: A 266 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7674 (ttt90) REVERT: B 6 GLN cc_start: 0.7165 (tt0) cc_final: 0.6138 (pm20) REVERT: B 59 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 217 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8222 (pmt) REVERT: G 21 MET cc_start: 0.7902 (tpp) cc_final: 0.7490 (tmt) REVERT: N 3 GLN cc_start: 0.7964 (tt0) cc_final: 0.7722 (tt0) outliers start: 14 outliers final: 6 residues processed: 146 average time/residue: 1.2963 time to fit residues: 199.5469 Evaluate side-chains 142 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 73 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 ASN A 35 GLN A 280 GLN G 59 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106430 restraints weight = 51492.464| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.75 r_work: 0.3071 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7860 Z= 0.137 Angle : 0.456 7.026 10670 Z= 0.251 Chirality : 0.040 0.142 1230 Planarity : 0.004 0.057 1351 Dihedral : 6.567 179.104 1097 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.58 % Allowed : 17.90 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 963 helix: 3.28 (0.26), residues: 381 sheet: 0.59 (0.32), residues: 231 loop : -0.35 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 343 PHE 0.011 0.001 PHE R 262 TYR 0.021 0.001 TYR N 60 ARG 0.015 0.000 ARG R 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.49 seconds wall clock time: 66 minutes 12.90 seconds (3972.90 seconds total)