Starting phenix.real_space_refine on Tue Feb 13 22:52:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgg_36233/02_2024/8jgg_36233_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5053 2.51 5 N 1362 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S GLU 46": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "R GLU 157": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7889 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1690 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2436 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 8, 'ASN%COO:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "R" Number of atoms: 1648 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Conformer: "B" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 bond proxies already assigned to first conformer: 1673 Conformer: "C" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 bond proxies already assigned to first conformer: 1673 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY R 276 " occ=0.13 ... (10 atoms not shown) pdb=" O CGLY R 276 " occ=0.74 Time building chain proxies: 6.00, per 1000 atoms: 0.76 Number of scatterers: 7889 At special positions: 0 Unit cell: (111.25, 102.35, 125.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1426 8.00 N 1362 7.00 C 5053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.95 Conformation dependent library (CDL) restraints added in 2.2 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 34.7% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.778A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.683A 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 'G' and resid 45 through 48 removed outlier: 3.942A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.542A pdb=" N GLU G 63 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 64 " --> pdb=" O PRO G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 59 through 64' Processing helix chain 'L' and resid 15 through 19 removed outlier: 4.053A pdb=" N LYS L 19 " --> pdb=" O ASP L 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.734A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.821A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.593A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.644A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.972A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.069A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.659A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 9 through 25 removed outlier: 3.676A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.000A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'R' and resid 29 through 33 removed outlier: 3.511A pdb=" N LEU R 33 " --> pdb=" O LEU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 52 removed outlier: 4.301A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 84 removed outlier: 3.524A pdb=" N ILE R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 126 removed outlier: 4.124A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP R 126 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 137 through 159 removed outlier: 3.767A pdb=" N LEU R 151 " --> pdb=" O TRP R 147 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET R 159 " --> pdb=" O ILE R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 203 removed outlier: 3.646A pdb=" N ILE R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 224 removed outlier: 3.703A pdb=" N LEU R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 236 removed outlier: 3.617A pdb=" N GLN R 235 " --> pdb=" O PRO R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 251 Processing helix chain 'R' and resid 254 through 273 Proline residue: R 269 - end of helix Processing sheet with id=AA1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.549A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AA4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.753A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.561A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.798A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.842A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.060A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.833A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.850A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AB3, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.637A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.995A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 975 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: 2.43 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1252 1.30 - 1.43: 2170 1.43 - 1.56: 4563 1.56 - 1.68: 1 1.68 - 1.81: 66 Bond restraints: 8052 Sorted by residual: bond pdb=" C HIS B 62 " pdb=" O HIS B 62 " ideal model delta sigma weight residual 1.234 1.174 0.060 1.22e-02 6.72e+03 2.41e+01 bond pdb=" CA GLN B 175 " pdb=" C GLN B 175 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.04e+01 bond pdb=" C ASN A 347 " pdb=" O ASN A 347 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.86e+01 bond pdb=" CA PHE A 223 " pdb=" C PHE A 223 " ideal model delta sigma weight residual 1.523 1.472 0.050 1.23e-02 6.61e+03 1.68e+01 bond pdb=" CA ASP B 66 " pdb=" C ASP B 66 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.31e-02 5.83e+03 1.67e+01 ... (remaining 8047 not shown) Histogram of bond angle deviations from ideal: 98.79 - 106.04: 137 106.04 - 113.30: 4426 113.30 - 120.55: 3305 120.55 - 127.81: 3012 127.81 - 135.06: 78 Bond angle restraints: 10958 Sorted by residual: angle pdb=" N THR R 34 " pdb=" CA THR R 34 " pdb=" C THR R 34 " ideal model delta sigma weight residual 112.89 99.76 13.13 1.24e+00 6.50e-01 1.12e+02 angle pdb=" N HIS R 252 " pdb=" CA HIS R 252 " pdb=" C HIS R 252 " ideal model delta sigma weight residual 113.55 101.39 12.16 1.26e+00 6.30e-01 9.31e+01 angle pdb=" N LYS A 10 " pdb=" CA LYS A 10 " pdb=" C LYS A 10 " ideal model delta sigma weight residual 113.50 103.02 10.48 1.23e+00 6.61e-01 7.25e+01 angle pdb=" N ALA A 7 " pdb=" CA ALA A 7 " pdb=" C ALA A 7 " ideal model delta sigma weight residual 113.41 103.66 9.75 1.22e+00 6.72e-01 6.39e+01 angle pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta sigma weight residual 119.76 112.95 6.81 1.00e+00 1.00e+00 4.63e+01 ... (remaining 10953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 4100 16.24 - 32.49: 439 32.49 - 48.73: 121 48.73 - 64.98: 21 64.98 - 81.22: 3 Dihedral angle restraints: 4684 sinusoidal: 1578 harmonic: 3106 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS S 35 " pdb=" C HIS S 35 " pdb=" N TRP S 36 " pdb=" CA TRP S 36 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1123 0.073 - 0.146: 147 0.146 - 0.220: 17 0.220 - 0.293: 1 0.293 - 0.366: 3 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA LEU A 348 " pdb=" N LEU A 348 " pdb=" C LEU A 348 " pdb=" CB LEU A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA HIS R 254 " pdb=" N HIS R 254 " pdb=" C HIS R 254 " pdb=" CB HIS R 254 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1288 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 19 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C LYS L 19 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS L 19 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG L 20 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 348 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C LEU A 348 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.35e+00 pdb=" C ILE B 232 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE B 232 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS B 233 " -0.012 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2391 2.81 - 3.33: 6758 3.33 - 3.86: 12570 3.86 - 4.38: 14371 4.38 - 4.90: 25872 Nonbonded interactions: 61962 Sorted by model distance: nonbonded pdb=" OG SER S 134 " pdb=" OE2 GLU S 234 " model vdw 2.288 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.296 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.319 2.520 nonbonded pdb=" O VAL R 253 " pdb=" OG SER R 257 " model vdw 2.334 2.440 nonbonded pdb=" N GLY B 185 " pdb=" OD1 ASP B 205 " model vdw 2.346 2.520 ... (remaining 61957 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=0.13 max=1.00 mean=1.00 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: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.470 Find NCS groups from input model: 0.260 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 8052 Z= 0.405 Angle : 0.941 13.129 10958 Z= 0.605 Chirality : 0.052 0.366 1291 Planarity : 0.004 0.042 1374 Dihedral : 14.774 81.222 2675 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.05 % Allowed : 24.47 % Favored : 74.47 % 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 (0.25), residues: 1054 helix: 0.24 (0.31), residues: 314 sheet: -0.45 (0.31), residues: 273 loop : -2.24 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 13 HIS 0.009 0.001 HIS B 183 PHE 0.015 0.001 PHE S 68 TYR 0.018 0.001 TYR S 60 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 186 ASP cc_start: 0.7487 (p0) cc_final: 0.6904 (p0) REVERT: R 79 ARG cc_start: 0.7649 (mmp80) cc_final: 0.7438 (mmp-170) REVERT: R 254 HIS cc_start: 0.3545 (OUTLIER) cc_final: 0.2345 (t-90) outliers start: 8 outliers final: 4 residues processed: 119 average time/residue: 0.9217 time to fit residues: 118.5370 Evaluate side-chains 98 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 250 PHE Chi-restraints excluded: chain R residue 254 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8052 Z= 0.235 Angle : 0.561 8.846 10958 Z= 0.296 Chirality : 0.043 0.136 1291 Planarity : 0.004 0.040 1374 Dihedral : 5.237 53.271 1153 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.95 % Allowed : 24.21 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1054 helix: 0.90 (0.31), residues: 323 sheet: -0.19 (0.30), residues: 272 loop : -2.08 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.002 PHE A 189 TYR 0.014 0.001 TYR S 178 ARG 0.002 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 86 LEU cc_start: 0.8099 (tp) cc_final: 0.7895 (mt) REVERT: B 134 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7228 (mtm110) REVERT: R 173 CYS cc_start: 0.6227 (t) cc_final: 0.5204 (m) REVERT: R 242 ILE cc_start: 0.8377 (pp) cc_final: 0.8035 (pt) outliers start: 30 outliers final: 15 residues processed: 128 average time/residue: 1.0520 time to fit residues: 143.7369 Evaluate side-chains 113 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 250 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8052 Z= 0.300 Angle : 0.581 9.265 10958 Z= 0.305 Chirality : 0.043 0.136 1291 Planarity : 0.004 0.047 1374 Dihedral : 4.803 47.670 1148 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.26 % Allowed : 24.87 % Favored : 69.87 % 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: -0.78 (0.26), residues: 1054 helix: 1.03 (0.31), residues: 322 sheet: -0.23 (0.29), residues: 281 loop : -1.87 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.002 PHE B 151 TYR 0.014 0.002 TYR R 106 ARG 0.002 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: R 173 CYS cc_start: 0.6162 (t) cc_final: 0.5156 (m) outliers start: 40 outliers final: 19 residues processed: 126 average time/residue: 1.0599 time to fit residues: 142.9480 Evaluate side-chains 117 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 250 PHE Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 27 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8052 Z= 0.227 Angle : 0.525 7.696 10958 Z= 0.278 Chirality : 0.042 0.135 1291 Planarity : 0.004 0.047 1374 Dihedral : 4.497 45.989 1147 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.26 % Allowed : 25.92 % Favored : 68.82 % 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: -0.58 (0.26), residues: 1054 helix: 1.25 (0.31), residues: 322 sheet: -0.18 (0.30), residues: 283 loop : -1.76 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE B 151 TYR 0.015 0.001 TYR R 99 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6055 (mpp80) REVERT: S 38 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7896 (ptt180) REVERT: A 18 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7779 (ttt) REVERT: B 134 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7208 (mtm110) REVERT: R 79 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6546 (tpm-80) REVERT: R 173 CYS cc_start: 0.6133 (t) cc_final: 0.5147 (m) outliers start: 40 outliers final: 21 residues processed: 127 average time/residue: 1.0502 time to fit residues: 142.6783 Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 ARG Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 250 PHE Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8052 Z= 0.324 Angle : 0.584 9.819 10958 Z= 0.306 Chirality : 0.044 0.138 1291 Planarity : 0.004 0.048 1374 Dihedral : 4.714 44.852 1147 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.00 % Allowed : 26.45 % Favored : 68.55 % 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: -0.65 (0.26), residues: 1054 helix: 1.24 (0.31), residues: 323 sheet: -0.25 (0.30), residues: 283 loop : -1.82 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.002 PHE B 151 TYR 0.015 0.002 TYR R 106 ARG 0.006 0.000 ARG R 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.5965 (mpp80) REVERT: S 38 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7964 (ptt180) REVERT: S 128 MET cc_start: 0.8540 (mmm) cc_final: 0.8130 (mmm) REVERT: A 33 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: B 134 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7156 (mtm110) REVERT: R 173 CYS cc_start: 0.6007 (t) cc_final: 0.5066 (m) outliers start: 38 outliers final: 23 residues processed: 124 average time/residue: 1.0803 time to fit residues: 142.8299 Evaluate side-chains 122 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 ARG Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 250 PHE Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 304 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8052 Z= 0.152 Angle : 0.484 7.171 10958 Z= 0.254 Chirality : 0.041 0.133 1291 Planarity : 0.003 0.045 1374 Dihedral : 4.147 42.864 1147 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.21 % Allowed : 27.50 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1054 helix: 1.59 (0.31), residues: 322 sheet: -0.01 (0.30), residues: 289 loop : -1.68 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.015 0.001 PHE R 104 TYR 0.016 0.001 TYR R 99 ARG 0.005 0.000 ARG R 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 128 MET cc_start: 0.8542 (mmm) cc_final: 0.8149 (mmm) REVERT: R 79 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6525 (tpm-80) REVERT: R 173 CYS cc_start: 0.6016 (t) cc_final: 0.5080 (m) outliers start: 32 outliers final: 18 residues processed: 119 average time/residue: 1.0036 time to fit residues: 128.1294 Evaluate side-chains 112 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8052 Z= 0.175 Angle : 0.496 7.051 10958 Z= 0.260 Chirality : 0.041 0.136 1291 Planarity : 0.003 0.044 1374 Dihedral : 3.863 18.327 1145 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.42 % Allowed : 28.95 % Favored : 67.63 % 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: -0.22 (0.26), residues: 1054 helix: 1.68 (0.31), residues: 317 sheet: -0.01 (0.30), residues: 294 loop : -1.64 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 104 TYR 0.014 0.001 TYR R 99 ARG 0.005 0.000 ARG R 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 20 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.5985 (mpp80) REVERT: S 128 MET cc_start: 0.8595 (mmm) cc_final: 0.8232 (mmm) REVERT: R 173 CYS cc_start: 0.6012 (t) cc_final: 0.5091 (m) outliers start: 26 outliers final: 19 residues processed: 108 average time/residue: 1.0553 time to fit residues: 121.8819 Evaluate side-chains 110 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 ARG Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8052 Z= 0.184 Angle : 0.504 7.976 10958 Z= 0.261 Chirality : 0.041 0.136 1291 Planarity : 0.003 0.044 1374 Dihedral : 3.865 18.287 1145 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.08 % Allowed : 27.76 % Favored : 68.16 % 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: -0.16 (0.26), residues: 1054 helix: 1.75 (0.31), residues: 317 sheet: 0.01 (0.30), residues: 295 loop : -1.60 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 104 TYR 0.013 0.001 TYR R 99 ARG 0.006 0.000 ARG R 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 128 MET cc_start: 0.8606 (mmm) cc_final: 0.8289 (mmm) REVERT: B 134 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7229 (mtm110) REVERT: R 79 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6523 (tpm-80) REVERT: R 173 CYS cc_start: 0.5975 (t) cc_final: 0.5087 (m) outliers start: 31 outliers final: 24 residues processed: 113 average time/residue: 1.0624 time to fit residues: 128.6608 Evaluate side-chains 115 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8052 Z= 0.199 Angle : 0.511 7.887 10958 Z= 0.267 Chirality : 0.042 0.136 1291 Planarity : 0.003 0.044 1374 Dihedral : 3.906 18.433 1145 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.68 % Allowed : 28.82 % Favored : 67.50 % 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: -0.22 (0.26), residues: 1054 helix: 1.65 (0.31), residues: 322 sheet: 0.03 (0.30), residues: 295 loop : -1.69 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 104 TYR 0.012 0.001 TYR R 106 ARG 0.005 0.000 ARG R 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 128 MET cc_start: 0.8614 (mmm) cc_final: 0.8331 (mmm) REVERT: A 18 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7737 (ttt) REVERT: B 134 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7248 (mtm110) REVERT: R 79 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6602 (tpm-80) REVERT: R 173 CYS cc_start: 0.6042 (t) cc_final: 0.5198 (m) outliers start: 28 outliers final: 24 residues processed: 113 average time/residue: 1.0896 time to fit residues: 132.2814 Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8052 Z= 0.186 Angle : 0.507 7.921 10958 Z= 0.262 Chirality : 0.041 0.135 1291 Planarity : 0.003 0.044 1374 Dihedral : 3.868 18.261 1145 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.68 % Allowed : 28.68 % Favored : 67.63 % 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: -0.17 (0.26), residues: 1054 helix: 1.69 (0.31), residues: 322 sheet: 0.07 (0.30), residues: 295 loop : -1.66 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE R 104 TYR 0.012 0.001 TYR S 178 ARG 0.005 0.000 ARG R 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 128 MET cc_start: 0.8614 (mmm) cc_final: 0.8338 (mmm) REVERT: A 18 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7741 (ttt) REVERT: B 134 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7250 (mtm110) REVERT: R 79 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6619 (tpm-80) REVERT: R 173 CYS cc_start: 0.6036 (t) cc_final: 0.5201 (m) outliers start: 28 outliers final: 24 residues processed: 112 average time/residue: 1.0565 time to fit residues: 126.5634 Evaluate side-chains 116 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118907 restraints weight = 9559.009| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.70 r_work: 0.3265 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8052 Z= 0.219 Angle : 0.521 7.834 10958 Z= 0.271 Chirality : 0.042 0.136 1291 Planarity : 0.003 0.045 1374 Dihedral : 3.955 18.651 1145 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.68 % Allowed : 28.68 % Favored : 67.63 % 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: -0.19 (0.26), residues: 1054 helix: 1.67 (0.31), residues: 322 sheet: 0.05 (0.30), residues: 295 loop : -1.66 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE B 151 TYR 0.013 0.001 TYR R 106 ARG 0.005 0.000 ARG R 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.95 seconds wall clock time: 54 minutes 39.03 seconds (3279.03 seconds total)