Starting phenix.real_space_refine on Thu Jan 18 18:17:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_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_33984/01_2024/7yon_33984_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_33984_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yon_33984/01_2024/7yon_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-1.21-5211/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: 5.08, 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: 3.14 Conformation dependent library (CDL) restraints added in 1.8 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: 1.69 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: 2.83 Time building geometry restraints manager: 3.47 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: 5012 17.51 - 35.03: 443 35.03 - 52.54: 81 52.54 - 70.05: 18 70.05 - 87.56: 5 Dihedral angle restraints: 5559 sinusoidal: 2171 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 5556 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: 7.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.700 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.800 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.270 ------------------------------------------------------------------------------- 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 : 13.649 87.563 3364 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 % Allowed : 0.20 % Favored : 99.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 354 TYR 0.021 0.001 TYR R 110 ARG 0.004 0.000 ARG B 19 *********************** 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 : 1.010 Fit side-chains REVERT: A 21 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7510 (mtm110) REVERT: A 209 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8792 (tttp) REVERT: B 134 ARG cc_start: 0.7950 (ptt90) cc_final: 0.7720 (ptt-90) REVERT: R 96 ASP cc_start: 0.7546 (m-30) cc_final: 0.7313 (m-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.2896 time to fit residues: 212.6755 Evaluate side-chains 137 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 0.9980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 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: 0.7478 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.1180 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= 0.217 Angle : 0.540 6.816 12659 Z= 0.285 Chirality : 0.042 0.154 1446 Planarity : 0.004 0.053 1591 Dihedral : 3.873 18.626 1265 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 9.47 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1145 helix: 1.86 (0.27), residues: 375 sheet: 1.23 (0.30), residues: 286 loop : -0.46 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS R 73 PHE 0.012 0.001 PHE A 189 TYR 0.017 0.002 TYR R 110 ARG 0.007 0.000 ARG B 19 *********************** 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 162 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7454 (mtm110) REVERT: A 209 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8796 (tttp) REVERT: B 20 ASP cc_start: 0.7243 (m-30) cc_final: 0.7022 (m-30) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 1.3547 time to fit residues: 214.6787 Evaluate side-chains 142 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.7887 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9347 Z= 0.226 Angle : 0.533 7.535 12659 Z= 0.278 Chirality : 0.042 0.154 1446 Planarity : 0.003 0.053 1591 Dihedral : 3.915 18.996 1265 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.39 % Allowed : 12.26 % Favored : 85.34 % 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: 1.28 (0.25), residues: 1145 helix: 2.15 (0.27), residues: 376 sheet: 1.17 (0.30), residues: 292 loop : -0.41 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.020 0.001 TYR R 110 ARG 0.005 0.000 ARG B 19 *********************** 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 158 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7410 (mtm110) REVERT: A 209 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8824 (tttp) outliers start: 24 outliers final: 11 residues processed: 142 average time/residue: 1.3116 time to fit residues: 198.1300 Evaluate side-chains 144 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 137 ASP 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: 0.0050 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9347 Z= 0.292 Angle : 0.578 7.845 12659 Z= 0.298 Chirality : 0.044 0.153 1446 Planarity : 0.004 0.055 1591 Dihedral : 4.091 22.800 1265 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.29 % Allowed : 13.36 % Favored : 83.35 % 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: 1.18 (0.25), residues: 1145 helix: 2.12 (0.28), residues: 376 sheet: 1.06 (0.30), residues: 283 loop : -0.45 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.002 PHE A 189 TYR 0.025 0.002 TYR R 110 ARG 0.006 0.000 ARG B 19 *********************** 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 165 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7398 (mtm110) REVERT: A 186 GLU cc_start: 0.7227 (tt0) cc_final: 0.6934 (tt0) REVERT: A 209 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8825 (tttp) REVERT: B 129 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7004 (tmt170) REVERT: L 24 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7586 (mm) REVERT: R 51 VAL cc_start: 0.8337 (m) cc_final: 0.7991 (t) outliers start: 33 outliers final: 16 residues processed: 146 average time/residue: 1.2954 time to fit residues: 201.1476 Evaluate side-chains 151 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 137 ASP 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 100 ASN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9347 Z= 0.192 Angle : 0.507 8.290 12659 Z= 0.265 Chirality : 0.042 0.154 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.914 22.874 1265 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.59 % Allowed : 15.35 % Favored : 82.05 % 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: 1.26 (0.25), residues: 1145 helix: 2.14 (0.28), residues: 384 sheet: 1.15 (0.30), residues: 286 loop : -0.44 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR R 110 ARG 0.006 0.000 ARG B 19 *********************** 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 165 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7393 (mtm110) REVERT: A 209 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8823 (tttp) REVERT: L 24 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7568 (mm) REVERT: R 51 VAL cc_start: 0.8308 (m) cc_final: 0.7973 (t) REVERT: R 98 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7608 (mm) outliers start: 26 outliers final: 15 residues processed: 154 average time/residue: 1.3456 time to fit residues: 220.2657 Evaluate side-chains 150 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR 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: 0.5980 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1702 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= 0.179 Angle : 0.503 8.807 12659 Z= 0.262 Chirality : 0.042 0.153 1446 Planarity : 0.003 0.054 1591 Dihedral : 3.876 22.273 1265 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.79 % Allowed : 15.15 % Favored : 82.05 % 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: 2.22 (0.28), residues: 385 sheet: 1.16 (0.30), residues: 286 loop : -0.44 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR R 110 ARG 0.005 0.000 ARG B 19 *********************** 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 162 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7380 (mtm110) REVERT: A 209 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8791 (tttp) REVERT: B 46 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7031 (mpt-90) REVERT: B 129 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6961 (tmt170) REVERT: L 24 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7560 (mm) REVERT: R 51 VAL cc_start: 0.8240 (m) cc_final: 0.7918 (t) REVERT: R 98 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7620 (mm) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 1.2816 time to fit residues: 206.1300 Evaluate side-chains 153 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 175 GLN R 100 ASN R 261 GLN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9347 Z= 0.234 Angle : 0.533 9.102 12659 Z= 0.276 Chirality : 0.043 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.963 23.564 1265 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.79 % Allowed : 16.35 % Favored : 80.86 % 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: 2.07 (0.28), residues: 391 sheet: 1.06 (0.30), residues: 286 loop : -0.48 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.017 0.001 TYR R 110 ARG 0.006 0.000 ARG B 19 *********************** 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 165 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7377 (mtm110) REVERT: A 209 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8792 (tttp) REVERT: B 46 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7046 (mpt-90) REVERT: B 129 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6950 (tmt170) REVERT: L 24 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7576 (mm) REVERT: R 51 VAL cc_start: 0.8246 (m) cc_final: 0.7935 (t) REVERT: R 98 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7587 (mm) outliers start: 28 outliers final: 17 residues processed: 153 average time/residue: 1.3124 time to fit residues: 213.4905 Evaluate side-chains 156 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 99 optimal weight: 0.0670 chunk 105 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN B 175 GLN R 100 ASN R 248 ASN R 261 GLN S 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1859 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= 0.141 Angle : 0.471 9.550 12659 Z= 0.247 Chirality : 0.041 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.758 21.698 1265 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.49 % Allowed : 16.75 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1145 helix: 2.34 (0.28), residues: 384 sheet: 1.17 (0.31), residues: 291 loop : -0.40 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 319 TYR 0.012 0.001 TYR S 235 ARG 0.004 0.000 ARG R 82 *********************** 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 161 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7367 (m-30) cc_final: 0.7150 (m-30) REVERT: A 21 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7359 (mtm110) REVERT: A 209 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8779 (tttp) REVERT: B 44 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: B 129 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6918 (tmt170) REVERT: B 322 ASP cc_start: 0.6278 (m-30) cc_final: 0.6040 (m-30) REVERT: L 24 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7561 (mm) REVERT: R 261 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5752 (mp10) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 1.3122 time to fit residues: 212.0151 Evaluate side-chains 153 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 261 GLN Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR 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: 1.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 175 GLN R 100 ASN R 248 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9347 Z= 0.210 Angle : 0.524 9.671 12659 Z= 0.273 Chirality : 0.042 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.838 22.096 1265 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.29 % Allowed : 17.85 % Favored : 79.86 % 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: 1.34 (0.25), residues: 1145 helix: 2.23 (0.28), residues: 385 sheet: 1.11 (0.30), residues: 291 loop : -0.39 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 260 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR R 110 ARG 0.004 0.000 ARG B 19 *********************** 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 157 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7354 (mtm110) REVERT: A 209 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8794 (tttp) REVERT: B 44 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: B 46 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7030 (mpt-90) REVERT: B 129 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6930 (tmt170) REVERT: B 322 ASP cc_start: 0.6262 (m-30) cc_final: 0.6022 (m-30) REVERT: L 24 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7586 (mm) REVERT: R 98 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7563 (mm) outliers start: 23 outliers final: 13 residues processed: 147 average time/residue: 1.3341 time to fit residues: 208.3872 Evaluate side-chains 151 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 90 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 175 GLN R 100 ASN R 248 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9347 Z= 0.185 Angle : 0.511 10.006 12659 Z= 0.266 Chirality : 0.042 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.840 22.357 1265 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.89 % Allowed : 18.25 % Favored : 79.86 % 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: 2.30 (0.28), residues: 384 sheet: 1.10 (0.30), residues: 291 loop : -0.41 (0.27), residues: 470 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 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR R 110 ARG 0.005 0.000 ARG B 19 ********************** 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 152 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7346 (mtm110) REVERT: A 209 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8797 (tttp) REVERT: B 44 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: B 129 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6927 (tmt170) REVERT: B 322 ASP cc_start: 0.6285 (m-30) cc_final: 0.6043 (m-30) REVERT: L 24 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7584 (mm) outliers start: 19 outliers final: 13 residues processed: 142 average time/residue: 1.3281 time to fit residues: 200.6678 Evaluate side-chains 148 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 175 GLN R 100 ASN R 248 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095956 restraints weight = 14231.760| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.63 r_work: 0.3068 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9347 Z= 0.233 Angle : 0.549 9.870 12659 Z= 0.284 Chirality : 0.043 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.945 23.839 1265 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 18.15 % Favored : 79.86 % 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: 1.25 (0.25), residues: 1145 helix: 2.13 (0.28), residues: 391 sheet: 1.06 (0.30), residues: 291 loop : -0.45 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.017 0.002 TYR R 110 ARG 0.005 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3946.73 seconds wall clock time: 70 minutes 38.48 seconds (4238.48 seconds total)