Starting phenix.real_space_refine on Sat Apr 6 08:58:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/04_2024/7piu_13453.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/04_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_13453/04_2024/7piu_13453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/04_2024/7piu_13453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/04_2024/7piu_13453.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7piu_13453/04_2024/7piu_13453.pdb" } 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 Residue "R GLU 49": "OE1" <-> "OE2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 305": "NH1" <-> "NH2" Residue "P ARG 1": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7788 Number of models: 1 Model: "" Number of chains: 12 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: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Classifications: {'peptide': 8} Modifications used: {'PEPT-D': 2} Link IDs: {'TRANS': 7} 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: 8.12, per 1000 atoms: 1.04 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 - 3.50 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: 3.08 Conformation dependent library (CDL) restraints added in 2.6 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: 0.72 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: 2.22 Time building geometry restraints manager: 3.30 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: 2131 1.44 - 1.57: 4396 1.57 - 1.69: 1 1.69 - 1.82: 86 Bond restraints: 7862 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 7857 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.85: 170 106.85 - 113.76: 4401 113.76 - 120.67: 3375 120.67 - 127.58: 2672 127.58 - 134.48: 58 Bond angle restraints: 10676 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 10671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 4640 35.97 - 71.95: 86 71.95 - 107.92: 4 107.92 - 143.89: 0 143.89 - 179.87: 1 Dihedral angle restraints: 4731 sinusoidal: 1818 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 4728 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 2.440 nonbonded pdb=" OD1 ASP G 48 " pdb=" O HOH G 101 " model vdw 2.280 2.440 nonbonded pdb=" O GLY B 64 " pdb=" O HOH B 401 " model vdw 2.335 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.343 2.440 ... (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 ========== 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: 0.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.740 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.910 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- 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 7862 Z= 0.855 Angle : 1.708 10.981 10676 Z= 1.284 Chirality : 0.094 0.343 1230 Planarity : 0.003 0.031 1353 Dihedral : 14.833 179.868 2834 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 : 0.854 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: 1.2505 time to fit residues: 246.8521 Evaluate side-chains 145 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 0.7980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 ASN A 357 ASN B 266 HIS B 340 ASN G 18 GLN N 31 ASN N 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7862 Z= 0.174 Angle : 0.500 4.462 10676 Z= 0.281 Chirality : 0.040 0.133 1230 Planarity : 0.004 0.029 1353 Dihedral : 7.036 179.483 1106 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.92 % Allowed : 12.30 % Favored : 84.77 % 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: 0.51 (0.25), residues: 963 helix: 1.58 (0.25), residues: 380 sheet: 0.15 (0.31), residues: 222 loop : -0.83 (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 0.010 0.001 TYR B 289 ARG 0.007 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 177 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.805 Fit side-chains REVERT: A 20 ARG cc_start: 0.6864 (mtp-110) cc_final: 0.6431 (mtm-85) REVERT: A 254 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: B 6 GLN cc_start: 0.6957 (tt0) cc_final: 0.5767 (pm20) REVERT: B 59 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8404 (t80) REVERT: B 217 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8303 (pmt) REVERT: G 21 MET cc_start: 0.7902 (tpp) cc_final: 0.7415 (tmt) REVERT: N 3 GLN cc_start: 0.7983 (tt0) cc_final: 0.7728 (tt0) REVERT: N 99 CYS cc_start: 0.7777 (m) cc_final: 0.7447 (m) outliers start: 23 outliers final: 6 residues processed: 162 average time/residue: 1.2541 time to fit residues: 214.6561 Evaluate side-chains 143 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 254 GLU 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 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: 0.0770 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 72 ASN A 253 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7862 Z= 0.138 Angle : 0.462 7.505 10676 Z= 0.256 Chirality : 0.040 0.174 1230 Planarity : 0.004 0.044 1353 Dihedral : 6.641 179.158 1099 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.05 % Allowed : 13.52 % Favored : 83.43 % 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: 1.35 (0.27), residues: 963 helix: 2.59 (0.26), residues: 380 sheet: 0.37 (0.32), residues: 222 loop : -0.61 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 343 PHE 0.013 0.001 PHE R 152 TYR 0.016 0.001 TYR N 60 ARG 0.012 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 162 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.822 Fit side-chains REVERT: A 20 ARG cc_start: 0.6809 (mtp-110) cc_final: 0.6394 (mtm-85) REVERT: A 25 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7735 (mptp) REVERT: B 6 GLN cc_start: 0.6982 (tt0) cc_final: 0.5876 (pm20) REVERT: B 59 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 217 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8319 (pmt) REVERT: G 21 MET cc_start: 0.7876 (tpp) cc_final: 0.7489 (tmt) REVERT: N 3 GLN cc_start: 0.7966 (tt0) cc_final: 0.7751 (tt0) outliers start: 24 outliers final: 9 residues processed: 149 average time/residue: 1.3683 time to fit residues: 214.7985 Evaluate side-chains 141 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 265 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7862 Z= 0.271 Angle : 0.522 6.670 10676 Z= 0.287 Chirality : 0.042 0.165 1230 Planarity : 0.004 0.037 1353 Dihedral : 6.831 177.303 1099 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.65 % Allowed : 14.25 % Favored : 82.10 % 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: 1.51 (0.27), residues: 963 helix: 2.66 (0.26), residues: 380 sheet: 0.49 (0.32), residues: 228 loop : -0.47 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 220 HIS 0.007 0.001 HIS A 343 PHE 0.018 0.002 PHE R 152 TYR 0.017 0.002 TYR N 60 ARG 0.007 0.001 ARG A 375 *********************** 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 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.825 Fit side-chains REVERT: A 20 ARG cc_start: 0.6846 (mtp-110) cc_final: 0.6400 (mtm-85) REVERT: A 25 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7804 (mptp) REVERT: A 376 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: B 6 GLN cc_start: 0.7041 (tt0) cc_final: 0.5928 (pm20) REVERT: B 59 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 217 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7919 (pmt) REVERT: G 21 MET cc_start: 0.7956 (tpp) cc_final: 0.7491 (tmt) REVERT: G 28 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8215 (pp) REVERT: N 3 GLN cc_start: 0.8053 (tt0) cc_final: 0.7796 (tt0) REVERT: N 89 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7561 (pm20) outliers start: 29 outliers final: 14 residues processed: 151 average time/residue: 1.3356 time to fit residues: 212.8623 Evaluate side-chains 150 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP Chi-restraints excluded: chain R residue 241 MET 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 193 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 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: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7862 Z= 0.201 Angle : 0.487 6.497 10676 Z= 0.268 Chirality : 0.041 0.156 1230 Planarity : 0.004 0.040 1353 Dihedral : 6.761 178.312 1099 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.05 % Allowed : 15.47 % Favored : 81.49 % 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: 1.70 (0.27), residues: 963 helix: 2.83 (0.26), residues: 380 sheet: 0.56 (0.32), residues: 232 loop : -0.39 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 343 PHE 0.014 0.002 PHE R 152 TYR 0.017 0.001 TYR N 60 ARG 0.014 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 158 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.778 Fit side-chains REVERT: A 20 ARG cc_start: 0.6839 (mtp-110) cc_final: 0.6413 (mtm-85) REVERT: A 25 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7744 (mptp) REVERT: B 6 GLN cc_start: 0.7088 (tt0) cc_final: 0.5998 (pm20) REVERT: B 59 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8319 (t80) REVERT: B 217 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8216 (pmt) REVERT: G 21 MET cc_start: 0.7946 (tpp) cc_final: 0.7499 (tmt) REVERT: G 28 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8213 (pp) REVERT: N 3 GLN cc_start: 0.8045 (tt0) cc_final: 0.7779 (tt0) outliers start: 23 outliers final: 12 residues processed: 144 average time/residue: 1.3731 time to fit residues: 208.4740 Evaluate side-chains 149 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP 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 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 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: 3.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 ASN A 257 ASN B 32 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7862 Z= 0.190 Angle : 0.476 6.476 10676 Z= 0.261 Chirality : 0.041 0.146 1230 Planarity : 0.004 0.038 1353 Dihedral : 6.727 178.400 1099 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.41 % Allowed : 15.71 % Favored : 80.88 % 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: 1.75 (0.27), residues: 963 helix: 2.94 (0.25), residues: 380 sheet: 0.43 (0.32), residues: 234 loop : -0.31 (0.33), residues: 349 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 0.023 0.002 PHE R 45 TYR 0.009 0.001 TYR A 344 ARG 0.007 0.001 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 164 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.885 Fit side-chains REVERT: A 20 ARG cc_start: 0.6807 (mtp-110) cc_final: 0.6393 (mtm-85) REVERT: A 25 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (mptp) REVERT: A 376 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: B 6 GLN cc_start: 0.7194 (tt0) cc_final: 0.6138 (pm20) REVERT: B 59 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8306 (t80) REVERT: B 217 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8208 (pmt) REVERT: G 21 MET cc_start: 0.7947 (tpp) cc_final: 0.7505 (tmt) REVERT: G 22 GLU cc_start: 0.8089 (pt0) cc_final: 0.7522 (tt0) REVERT: G 28 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8202 (pp) REVERT: N 3 GLN cc_start: 0.8043 (tt0) cc_final: 0.7824 (tt0) outliers start: 26 outliers final: 16 residues processed: 149 average time/residue: 1.3786 time to fit residues: 216.5516 Evaluate side-chains 156 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP 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 320 VAL 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 228 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7862 Z= 0.162 Angle : 0.458 6.315 10676 Z= 0.251 Chirality : 0.040 0.140 1230 Planarity : 0.004 0.047 1353 Dihedral : 6.662 178.933 1099 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.80 % Allowed : 16.44 % 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: 1.84 (0.27), residues: 963 helix: 3.07 (0.25), residues: 380 sheet: 0.41 (0.32), residues: 234 loop : -0.29 (0.33), residues: 349 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 0.012 0.001 PHE R 262 TYR 0.018 0.001 TYR N 60 ARG 0.014 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 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.873 Fit side-chains REVERT: A 20 ARG cc_start: 0.6834 (mtp-110) cc_final: 0.6419 (mtm-85) REVERT: A 25 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7709 (mptp) REVERT: B 6 GLN cc_start: 0.7185 (tt0) cc_final: 0.6126 (pm20) REVERT: B 59 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8207 (pmt) REVERT: G 21 MET cc_start: 0.7940 (tpp) cc_final: 0.7470 (tmt) REVERT: G 22 GLU cc_start: 0.8032 (pt0) cc_final: 0.7640 (tt0) REVERT: G 28 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8191 (pp) REVERT: N 3 GLN cc_start: 0.7992 (tt0) cc_final: 0.7765 (tt0) outliers start: 21 outliers final: 11 residues processed: 148 average time/residue: 1.3714 time to fit residues: 213.9811 Evaluate side-chains 153 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP 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 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 56 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7862 Z= 0.134 Angle : 0.446 6.200 10676 Z= 0.244 Chirality : 0.040 0.136 1230 Planarity : 0.003 0.035 1353 Dihedral : 6.579 179.278 1099 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.44 % Allowed : 17.30 % Favored : 80.27 % 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: 1.97 (0.27), residues: 963 helix: 3.19 (0.25), residues: 380 sheet: 0.46 (0.32), residues: 234 loop : -0.23 (0.33), residues: 349 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 0.018 0.001 PHE R 45 TYR 0.019 0.001 TYR N 60 ARG 0.008 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 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.895 Fit side-chains REVERT: A 20 ARG cc_start: 0.6838 (mtp-110) cc_final: 0.6421 (mtm-85) REVERT: A 25 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7688 (mptp) REVERT: B 6 GLN cc_start: 0.7174 (tt0) cc_final: 0.6135 (pm20) REVERT: B 59 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 217 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7921 (pmt) REVERT: G 21 MET cc_start: 0.7930 (tpp) cc_final: 0.7500 (tmt) REVERT: G 22 GLU cc_start: 0.7969 (pt0) cc_final: 0.7673 (tt0) REVERT: G 28 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8228 (pp) REVERT: N 3 GLN cc_start: 0.7984 (tt0) cc_final: 0.7770 (tt0) outliers start: 18 outliers final: 10 residues processed: 153 average time/residue: 1.3477 time to fit residues: 217.2702 Evaluate side-chains 158 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP 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 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP 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: 0.8980 chunk 83 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7862 Z= 0.164 Angle : 0.460 6.229 10676 Z= 0.252 Chirality : 0.040 0.137 1230 Planarity : 0.003 0.037 1353 Dihedral : 6.612 178.704 1099 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.31 % Allowed : 17.54 % Favored : 80.15 % 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: 1.97 (0.27), residues: 963 helix: 3.14 (0.25), residues: 381 sheet: 0.53 (0.32), residues: 238 loop : -0.22 (0.33), residues: 344 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 0.011 0.002 PHE R 262 TYR 0.021 0.001 TYR N 60 ARG 0.009 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 157 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.710 Fit side-chains REVERT: A 20 ARG cc_start: 0.6840 (mtp-110) cc_final: 0.6442 (mtm-85) REVERT: A 25 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7698 (mptp) REVERT: B 6 GLN cc_start: 0.7161 (tt0) cc_final: 0.6116 (pm20) REVERT: B 59 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 217 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8191 (pmt) REVERT: G 21 MET cc_start: 0.7936 (tpp) cc_final: 0.7502 (tmt) REVERT: G 22 GLU cc_start: 0.7971 (pt0) cc_final: 0.7646 (tt0) REVERT: G 28 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8181 (pp) REVERT: N 3 GLN cc_start: 0.7977 (tt0) cc_final: 0.7761 (tt0) REVERT: N 43 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7944 (mtmm) outliers start: 17 outliers final: 11 residues processed: 148 average time/residue: 1.3431 time to fit residues: 209.4307 Evaluate side-chains 154 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP Chi-restraints excluded: chain R residue 241 MET 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 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP 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: 0.6980 chunk 41 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7862 Z= 0.139 Angle : 0.449 6.216 10676 Z= 0.246 Chirality : 0.040 0.137 1230 Planarity : 0.004 0.062 1353 Dihedral : 6.583 179.168 1099 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 17.90 % Favored : 79.90 % 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: 2.04 (0.27), residues: 963 helix: 3.20 (0.25), residues: 381 sheet: 0.57 (0.32), residues: 238 loop : -0.20 (0.34), residues: 344 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 0.012 0.001 PHE R 262 TYR 0.020 0.001 TYR N 60 ARG 0.016 0.001 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 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.897 Fit side-chains REVERT: A 20 ARG cc_start: 0.6818 (mtp-110) cc_final: 0.6411 (mtm-85) REVERT: A 25 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7732 (mptp) REVERT: B 6 GLN cc_start: 0.7176 (tt0) cc_final: 0.6140 (pm20) REVERT: B 59 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8260 (t80) REVERT: B 217 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8200 (pmt) REVERT: G 21 MET cc_start: 0.7932 (tpp) cc_final: 0.7501 (tmt) REVERT: G 22 GLU cc_start: 0.7962 (pt0) cc_final: 0.7670 (tt0) REVERT: G 28 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8215 (pp) REVERT: N 3 GLN cc_start: 0.7970 (tt0) cc_final: 0.7751 (tt0) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 1.3798 time to fit residues: 217.6535 Evaluate side-chains 159 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 189 ASP Chi-restraints excluded: chain R residue 241 MET 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 31 GLN Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 320 VAL 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 228 ASP 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 22 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103968 restraints weight = 49171.867| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.74 r_work: 0.3016 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7862 Z= 0.176 Angle : 0.467 6.208 10676 Z= 0.256 Chirality : 0.040 0.137 1230 Planarity : 0.003 0.037 1353 Dihedral : 6.624 178.496 1099 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.19 % Allowed : 17.90 % Favored : 79.90 % 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: 2.00 (0.27), residues: 963 helix: 3.15 (0.25), residues: 381 sheet: 0.57 (0.32), residues: 238 loop : -0.20 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 343 PHE 0.011 0.002 PHE R 262 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.001 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.80 seconds wall clock time: 68 minutes 44.08 seconds (4124.08 seconds total)