Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 06:04:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/08_2023/7yon_33984_updated.pdb" } resolution = 2.95 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= 0.009 sd= 0.033 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 61 5.16 5 C 5839 2.51 5 N 1555 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R GLU 157": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 223 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain breaks: 1 Chain: "R" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2402 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.55 Number of scatterers: 9161 At special positions: 0 Unit cell: (95.937, 121.407, 140.085, 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 61 16.00 O 1706 8.00 N 1555 7.00 C 5839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 14 sheets defined 34.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.565A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 4.019A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.211A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.816A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.504A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.583A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'L' and resid 18 through 31 removed outlier: 3.678A pdb=" N ALA L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 45 No H-bonds generated for 'chain 'R' and resid 43 through 45' Processing helix chain 'R' and resid 47 through 77 removed outlier: 3.908A pdb=" N VAL R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE R 72 " --> pdb=" O ASN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 removed outlier: 3.533A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN R 100 " --> pdb=" O ASP R 96 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 120 through 123 No H-bonds generated for 'chain 'R' and resid 120 through 123' Processing helix chain 'R' and resid 126 through 153 removed outlier: 3.570A pdb=" N ILE R 144 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 179 Processing helix chain 'R' and resid 181 through 185 Processing helix chain 'R' and resid 214 through 227 removed outlier: 3.899A pdb=" N SER R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 247 Processing helix chain 'R' and resid 256 through 293 removed outlier: 3.634A pdb=" N HIS R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG R 262 " --> pdb=" O HIS R 258 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS R 272 " --> pdb=" O LYS R 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL R 273 " --> pdb=" O MET R 269 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.502A pdb=" N GLN R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 325 removed outlier: 4.511A pdb=" N SER R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE R 319 " --> pdb=" O MET R 315 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 330 through 340 removed outlier: 3.517A pdb=" N ALA R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.681A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.998A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.841A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.840A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.913A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.759A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.707A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.657A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 187 through 192 Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.509A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 140 through 142 removed outlier: 4.055A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.570A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.640A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1110 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: 2.61 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1479 1.31 - 1.43: 2566 1.43 - 1.56: 5215 1.56 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9347 Sorted by residual: bond pdb=" C VAL S 149 " pdb=" N THR S 150 " ideal model delta sigma weight residual 1.333 1.367 -0.035 2.74e-02 1.33e+03 1.60e+00 bond pdb=" CG PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.34e-01 bond pdb=" CG1 ILE S 51 " pdb=" CD1 ILE S 51 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.74e-01 bond pdb=" CA THR A 4 " pdb=" CB THR A 4 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.69e-02 3.50e+03 3.58e-01 bond pdb=" C SER R 181 " pdb=" N PRO R 182 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.19e-02 7.06e+03 3.42e-01 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 199 106.67 - 113.50: 5149 113.50 - 120.33: 3284 120.33 - 127.16: 3930 127.16 - 134.00: 97 Bond angle restraints: 12659 Sorted by residual: angle pdb=" CE2 TYC L 36 " pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 129.45 120.15 9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CE1 TYC L 36 " pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 110.51 119.75 -9.24 3.00e+00 1.11e-01 9.49e+00 angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.32 112.45 -4.13 1.64e+00 3.72e-01 6.35e+00 angle pdb=" N GLU L 6 " pdb=" CA GLU L 6 " pdb=" CB GLU L 6 " ideal model delta sigma weight residual 113.65 110.19 3.46 1.47e+00 4.63e-01 5.53e+00 angle pdb=" C VAL S 149 " pdb=" N THR S 150 " pdb=" CA THR S 150 " ideal model delta sigma weight residual 122.15 130.17 -8.02 3.47e+00 8.31e-02 5.34e+00 ... (remaining 12654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5011 17.51 - 35.03: 442 35.03 - 52.54: 81 52.54 - 70.05: 18 70.05 - 87.56: 5 Dihedral angle restraints: 5557 sinusoidal: 2169 harmonic: 3388 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.94 -56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual 180.00 135.31 44.69 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" CD GLU A 298 " pdb=" OE1 GLU A 298 " ideal model delta sinusoidal sigma weight residual 0.00 86.42 -86.42 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 882 0.031 - 0.061: 394 0.061 - 0.092: 98 0.092 - 0.123: 65 0.123 - 0.154: 7 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA ILE R 195 " pdb=" N ILE R 195 " pdb=" C ILE R 195 " pdb=" CB ILE R 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE S 157 " pdb=" N ILE S 157 " pdb=" C ILE S 157 " pdb=" CB ILE S 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1443 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 195 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO R 196 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 184 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO S 185 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO S 185 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO S 185 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 110 " 0.011 2.00e-02 2.50e+03 8.79e-03 1.55e+00 pdb=" CG TYR R 110 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR R 110 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR R 110 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 110 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 110 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 181 2.70 - 3.25: 8421 3.25 - 3.80: 13242 3.80 - 4.35: 17864 4.35 - 4.90: 31280 Nonbonded interactions: 70988 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" N ASP B 154 " model vdw 2.195 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.196 2.440 nonbonded pdb=" NE2 GLN S 179 " pdb=" O GLN S 183 " model vdw 2.320 2.520 nonbonded pdb=" OE1 GLN L 34 " pdb=" O HOH L 101 " model vdw 2.323 2.440 ... (remaining 70983 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=1.00 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 14.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.160 Find NCS groups from input model: 0.260 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.003 0.035 9347 Z= 0.186 Angle : 0.498 9.296 12659 Z= 0.251 Chirality : 0.041 0.154 1446 Planarity : 0.003 0.052 1591 Dihedral : 13.647 87.563 3362 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1145 helix: 0.14 (0.24), residues: 394 sheet: 1.23 (0.31), residues: 282 loop : -0.46 (0.27), residues: 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.2483 time to fit residues: 206.0542 Evaluate side-chains 135 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 230 ASN B 340 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9347 Z= 0.213 Angle : 0.543 6.888 12659 Z= 0.287 Chirality : 0.043 0.155 1446 Planarity : 0.004 0.053 1591 Dihedral : 3.820 17.187 1263 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.60 % 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: 1.16 (0.24), residues: 1145 helix: 1.95 (0.27), residues: 375 sheet: 1.25 (0.31), residues: 286 loop : -0.46 (0.26), residues: 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 148 average time/residue: 1.2465 time to fit residues: 196.6387 Evaluate side-chains 141 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 0.3826 time to fit residues: 4.1254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 331 ASN B 175 GLN R 100 ASN S 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9347 Z= 0.258 Angle : 0.557 7.527 12659 Z= 0.289 Chirality : 0.043 0.154 1446 Planarity : 0.004 0.053 1591 Dihedral : 3.959 19.858 1263 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.59 % 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: 1.22 (0.25), residues: 1145 helix: 2.13 (0.27), residues: 376 sheet: 1.14 (0.30), residues: 287 loop : -0.45 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 1.2433 time to fit residues: 190.8147 Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.2778 time to fit residues: 3.8354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN S 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 9347 Z= 0.367 Angle : 0.625 8.666 12659 Z= 0.320 Chirality : 0.045 0.157 1446 Planarity : 0.004 0.055 1591 Dihedral : 4.201 24.781 1263 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 3.19 % 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: 1.06 (0.25), residues: 1145 helix: 2.00 (0.27), residues: 376 sheet: 0.99 (0.30), residues: 283 loop : -0.50 (0.27), residues: 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.025 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 150 average time/residue: 1.2816 time to fit residues: 204.8314 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.3771 time to fit residues: 4.6264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 175 GLN R 100 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9347 Z= 0.182 Angle : 0.509 8.262 12659 Z= 0.266 Chirality : 0.042 0.155 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.936 24.241 1263 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 2.39 % 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: 1.27 (0.25), residues: 1145 helix: 2.18 (0.28), residues: 383 sheet: 1.11 (0.30), residues: 286 loop : -0.43 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 1.2691 time to fit residues: 203.0289 Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.1280 time to fit residues: 2.3467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9347 Z= 0.297 Angle : 0.582 8.695 12659 Z= 0.300 Chirality : 0.044 0.153 1446 Planarity : 0.004 0.055 1591 Dihedral : 4.099 26.288 1263 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.79 % 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: 1.13 (0.25), residues: 1145 helix: 2.10 (0.28), residues: 382 sheet: 0.98 (0.30), residues: 283 loop : -0.49 (0.27), residues: 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.940 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 147 average time/residue: 1.3090 time to fit residues: 205.2300 Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.4443 time to fit residues: 4.0436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN R 248 ASN R 261 GLN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9347 Z= 0.175 Angle : 0.505 9.052 12659 Z= 0.264 Chirality : 0.042 0.154 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.915 25.116 1263 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.99 % 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: 1.31 (0.25), residues: 1145 helix: 2.27 (0.28), residues: 383 sheet: 1.12 (0.30), residues: 286 loop : -0.44 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 147 average time/residue: 1.2739 time to fit residues: 200.1611 Evaluate side-chains 145 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.1453 time to fit residues: 1.9926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN R 248 ASN R 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9347 Z= 0.244 Angle : 0.548 9.367 12659 Z= 0.284 Chirality : 0.043 0.153 1446 Planarity : 0.003 0.055 1591 Dihedral : 4.008 26.114 1263 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.99 % 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: 1.19 (0.25), residues: 1145 helix: 2.17 (0.28), residues: 384 sheet: 1.00 (0.30), residues: 286 loop : -0.49 (0.27), residues: 475 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.025 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 1.3117 time to fit residues: 208.3079 Evaluate side-chains 147 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.1342 time to fit residues: 2.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 0.0060 chunk 67 optimal weight: 0.0870 chunk 108 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 overall best weight: 0.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 175 GLN R 100 ASN R 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 9347 Z= 0.118 Angle : 0.457 9.993 12659 Z= 0.240 Chirality : 0.040 0.152 1446 Planarity : 0.003 0.054 1591 Dihedral : 3.690 21.531 1263 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.30 % 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 (0.25), residues: 1145 helix: 2.28 (0.28), residues: 390 sheet: 1.16 (0.31), residues: 285 loop : -0.47 (0.27), residues: 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 144 average time/residue: 1.3372 time to fit residues: 205.7852 Evaluate side-chains 143 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.1787 time to fit residues: 2.0490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 113 optimal weight: 0.2980 chunk 104 optimal weight: 20.0000 chunk 90 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN R 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9347 Z= 0.145 Angle : 0.486 9.817 12659 Z= 0.253 Chirality : 0.041 0.151 1446 Planarity : 0.003 0.053 1591 Dihedral : 3.683 19.845 1263 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.50 % 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: 1.45 (0.25), residues: 1145 helix: 2.37 (0.28), residues: 385 sheet: 1.16 (0.31), residues: 290 loop : -0.37 (0.27), residues: 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 1.3049 time to fit residues: 200.4478 Evaluate side-chains 140 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 1.1263 time to fit residues: 5.0942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN R 248 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101345 restraints weight = 14235.915| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.59 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9347 Z= 0.208 Angle : 0.540 9.785 12659 Z= 0.279 Chirality : 0.042 0.151 1446 Planarity : 0.003 0.054 1591 Dihedral : 3.798 21.137 1263 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.69 % 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: 1.36 (0.25), residues: 1145 helix: 2.34 (0.28), residues: 384 sheet: 1.07 (0.31), residues: 285 loop : -0.39 (0.27), residues: 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.93 seconds wall clock time: 71 minutes 30.16 seconds (4290.16 seconds total)