Starting phenix.real_space_refine on Wed Feb 14 07:58:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na8_24268/02_2024/7na8_24268_updated.pdb" } resolution = 2.7 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= 0.004 sd= 0.074 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 63 5.16 5 C 5687 2.51 5 N 1502 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 220": "OE1" <-> "OE2" Residue "R GLU 124": "OE1" <-> "OE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "R GLU 296": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} 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: "N" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2350 Unusual residues: {'1KD': 1, 'CLR': 1} Classifications: {'peptide': 285, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273, None: 2} Not linked: pdbres="PHE R 340 " pdbres="1KD R 401 " Not linked: pdbres="1KD R 401 " pdbres="CLR R 402 " Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8888 At special positions: 0 Unit cell: (90.034, 122.248, 126.378, 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 63 16.00 O 1636 8.00 N 1502 7.00 C 5687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.12 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 34.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.638A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.449A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (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 280 removed outlier: 4.003A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (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 308 removed outlier: 3.861A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 removed outlier: 4.506A pdb=" N VAL A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 removed outlier: 4.068A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (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 12 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.570A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (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 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'R' and resid 41 through 70 removed outlier: 4.645A pdb=" N THR R 47 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU R 62 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU R 63 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET R 65 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER R 69 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG R 70 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 79 through 104 Proline residue: R 97 - end of helix removed outlier: 3.590A pdb=" N VAL R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU R 103 " --> pdb=" O ASP R 99 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 146 removed outlier: 3.573A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 124 " --> pdb=" O GLN R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 Processing helix chain 'R' and resid 159 through 174 Processing helix chain 'R' and resid 177 through 181 removed outlier: 3.876A pdb=" N LEU R 181 " --> pdb=" O ILE R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 195 No H-bonds generated for 'chain 'R' and resid 193 through 195' Processing helix chain 'R' and resid 202 through 206 Processing helix chain 'R' and resid 210 through 242 removed outlier: 3.850A pdb=" N TRP R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 4.010A pdb=" N VAL R 230 " --> pdb=" O PHE R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 285 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 323 removed outlier: 3.904A pdb=" N TYR R 303 " --> pdb=" O GLN R 299 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Proline residue: R 320 - end of helix removed outlier: 3.625A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 337 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.576A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.818A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.727A 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: 6.832A 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: 6.481A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.794A 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: 6.613A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.797A 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: 6.687A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.438A 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: 6.669A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.822A 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: 6.602A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.169A 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: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.770A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 146 through 148 removed outlier: 6.336A pdb=" N LYS N 244 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY N 225 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU N 178 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU N 187 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG N 180 " --> pdb=" O PRO N 185 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 155 through 160 removed outlier: 3.552A pdb=" N ALA N 211 " --> pdb=" O SER N 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 182 through 184 removed outlier: 3.623A pdb=" N ARG R 199 " --> pdb=" O GLY R 183 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1002 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: 2.42 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1424 1.29 - 1.42: 2422 1.42 - 1.56: 5143 1.56 - 1.69: 1 1.69 - 1.82: 90 Bond restraints: 9080 Sorted by residual: bond pdb=" N PRO R 278 " pdb=" CD PRO R 278 " ideal model delta sigma weight residual 1.473 1.194 0.279 1.40e-02 5.10e+03 3.97e+02 bond pdb=" N PRO R 39 " pdb=" CD PRO R 39 " ideal model delta sigma weight residual 1.473 1.343 0.130 1.40e-02 5.10e+03 8.57e+01 bond pdb=" CA SER R 308 " pdb=" CB SER R 308 " ideal model delta sigma weight residual 1.529 1.418 0.111 1.64e-02 3.72e+03 4.55e+01 bond pdb=" CA ASN A 294 " pdb=" C ASN A 294 " ideal model delta sigma weight residual 1.527 1.602 -0.075 1.19e-02 7.06e+03 3.97e+01 bond pdb=" C PHE N 32 " pdb=" O PHE N 32 " ideal model delta sigma weight residual 1.236 1.163 0.073 1.21e-02 6.83e+03 3.64e+01 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 92.66 - 100.93: 26 100.93 - 109.20: 731 109.20 - 117.47: 5808 117.47 - 125.74: 5592 125.74 - 134.01: 142 Bond angle restraints: 12299 Sorted by residual: angle pdb=" N THR A 295 " pdb=" CA THR A 295 " pdb=" C THR A 295 " ideal model delta sigma weight residual 110.14 96.39 13.75 1.55e+00 4.16e-01 7.87e+01 angle pdb=" C PHE R 279 " pdb=" CA PHE R 279 " pdb=" CB PHE R 279 " ideal model delta sigma weight residual 110.96 99.63 11.33 1.54e+00 4.22e-01 5.41e+01 angle pdb=" C22 1KD R 401 " pdb=" C23 1KD R 401 " pdb=" C26 1KD R 401 " ideal model delta sigma weight residual 109.58 131.07 -21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C LYS N 244 " pdb=" CA LYS N 244 " pdb=" CB LYS N 244 " ideal model delta sigma weight residual 109.75 98.13 11.62 1.65e+00 3.67e-01 4.96e+01 angle pdb=" C24 1KD R 401 " pdb=" C23 1KD R 401 " pdb=" C26 1KD R 401 " ideal model delta sigma weight residual 113.62 92.66 20.96 3.00e+00 1.11e-01 4.88e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 5132 23.74 - 47.47: 279 47.47 - 71.21: 33 71.21 - 94.94: 10 94.94 - 118.68: 3 Dihedral angle restraints: 5457 sinusoidal: 2204 harmonic: 3253 Sorted by residual: dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -162.31 76.31 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" C ASN R 305 " pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" CB ASN R 305 " ideal model delta harmonic sigma weight residual -122.60 -143.14 20.54 0 2.50e+00 1.60e-01 6.75e+01 dihedral pdb=" C LYS N 244 " pdb=" N LYS N 244 " pdb=" CA LYS N 244 " pdb=" CB LYS N 244 " ideal model delta harmonic sigma weight residual -122.60 -104.95 -17.65 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1365 0.145 - 0.289: 17 0.289 - 0.434: 8 0.434 - 0.579: 0 0.579 - 0.724: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASN R 305 " pdb=" N ASN R 305 " pdb=" C ASN R 305 " pdb=" CB ASN R 305 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA PHE R 279 " pdb=" N PHE R 279 " pdb=" C PHE R 279 " pdb=" CB PHE R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU R 42 " pdb=" N LEU R 42 " pdb=" C LEU R 42 " pdb=" CB LEU R 42 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1388 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 112 " -0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C GLY R 112 " 0.091 2.00e-02 2.50e+03 pdb=" O GLY R 112 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP R 113 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 221 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ALA N 221 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA N 221 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU N 222 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 115 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C LEU R 115 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU R 115 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS R 116 " 0.020 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 195 2.67 - 3.23: 8415 3.23 - 3.78: 13867 3.78 - 4.34: 20452 4.34 - 4.90: 33318 Nonbonded interactions: 76247 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.212 2.440 nonbonded pdb=" O PHE R 286 " pdb=" OG SER R 287 " model vdw 2.252 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.266 2.440 ... (remaining 76242 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: 1.530 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: 7.180 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.007 0.279 9080 Z= 0.455 Angle : 0.926 21.491 12299 Z= 0.560 Chirality : 0.060 0.724 1391 Planarity : 0.005 0.056 1538 Dihedral : 15.005 118.678 3346 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.31 % Allowed : 1.14 % Favored : 98.55 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 3.33 % 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: -1.04 (0.24), residues: 1102 helix: -0.42 (0.27), residues: 385 sheet: -0.53 (0.30), residues: 281 loop : -0.83 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.023 0.002 PHE R 279 TYR 0.022 0.002 TYR R 284 ARG 0.005 0.000 ARG N 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.998 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 1.4679 time to fit residues: 202.9526 Evaluate side-chains 106 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9080 Z= 0.223 Angle : 0.562 6.349 12299 Z= 0.293 Chirality : 0.043 0.142 1391 Planarity : 0.004 0.048 1538 Dihedral : 6.925 74.529 1331 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.45 % Allowed : 9.74 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.63 (0.24), residues: 1102 helix: 0.17 (0.27), residues: 380 sheet: -0.49 (0.30), residues: 285 loop : -0.72 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.023 0.001 PHE R 54 TYR 0.022 0.001 TYR R 284 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.031 Fit side-chains REVERT: B 325 MET cc_start: 0.8774 (tpp) cc_final: 0.8521 (tpt) outliers start: 14 outliers final: 7 residues processed: 115 average time/residue: 1.3560 time to fit residues: 165.6848 Evaluate side-chains 109 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS R 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9080 Z= 0.225 Angle : 0.534 5.974 12299 Z= 0.279 Chirality : 0.042 0.139 1391 Planarity : 0.004 0.045 1538 Dihedral : 6.662 70.678 1331 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 12.95 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.43 (0.25), residues: 1102 helix: 0.37 (0.27), residues: 378 sheet: -0.44 (0.29), residues: 285 loop : -0.59 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 54 TYR 0.014 0.001 TYR R 313 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.074 Fit side-chains REVERT: B 325 MET cc_start: 0.8762 (tpp) cc_final: 0.8480 (tpt) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 1.2780 time to fit residues: 152.5341 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9080 Z= 0.277 Angle : 0.554 6.547 12299 Z= 0.290 Chirality : 0.043 0.170 1391 Planarity : 0.004 0.041 1538 Dihedral : 6.721 71.481 1331 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 14.51 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.39 (0.25), residues: 1102 helix: 0.45 (0.27), residues: 377 sheet: -0.46 (0.29), residues: 291 loop : -0.56 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 280 PHE 0.012 0.001 PHE R 309 TYR 0.022 0.002 TYR R 284 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.096 Fit side-chains REVERT: B 325 MET cc_start: 0.8783 (tpp) cc_final: 0.8525 (tpt) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 1.3775 time to fit residues: 161.1496 Evaluate side-chains 106 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.0030 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 294 ASN R 110 ASN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9080 Z= 0.158 Angle : 0.506 8.902 12299 Z= 0.262 Chirality : 0.041 0.155 1391 Planarity : 0.003 0.038 1538 Dihedral : 6.064 66.387 1331 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.66 % Allowed : 16.17 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.12 (0.25), residues: 1102 helix: 0.79 (0.28), residues: 370 sheet: -0.32 (0.30), residues: 272 loop : -0.51 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 280 PHE 0.014 0.001 PHE R 54 TYR 0.018 0.001 TYR A 296 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.989 Fit side-chains REVERT: B 325 MET cc_start: 0.8729 (tpp) cc_final: 0.8375 (tpt) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.3308 time to fit residues: 154.3607 Evaluate side-chains 99 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9080 Z= 0.269 Angle : 0.552 8.863 12299 Z= 0.286 Chirality : 0.043 0.156 1391 Planarity : 0.004 0.035 1538 Dihedral : 6.432 69.640 1331 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.18 % Allowed : 16.58 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1102 helix: 0.72 (0.28), residues: 371 sheet: -0.34 (0.29), residues: 286 loop : -0.52 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.024 0.002 TYR R 284 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.010 Fit side-chains REVERT: A 271 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7260 (ttpt) REVERT: B 325 MET cc_start: 0.8767 (tpp) cc_final: 0.8486 (tpt) REVERT: N 93 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8145 (ttp) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 1.3652 time to fit residues: 159.9973 Evaluate side-chains 107 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 227 CYS Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9080 Z= 0.169 Angle : 0.512 8.212 12299 Z= 0.267 Chirality : 0.041 0.148 1391 Planarity : 0.003 0.034 1538 Dihedral : 6.015 65.675 1331 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 17.62 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.02 (0.25), residues: 1102 helix: 0.98 (0.28), residues: 367 sheet: -0.32 (0.29), residues: 287 loop : -0.51 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.015 0.001 TYR A 296 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.995 Fit side-chains REVERT: B 325 MET cc_start: 0.8741 (tpp) cc_final: 0.8385 (tpt) REVERT: N 93 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8083 (ttp) REVERT: R 73 GLU cc_start: 0.7699 (pm20) cc_final: 0.7200 (pm20) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 1.2696 time to fit residues: 150.2160 Evaluate side-chains 104 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.0770 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9080 Z= 0.210 Angle : 0.528 8.136 12299 Z= 0.274 Chirality : 0.042 0.144 1391 Planarity : 0.003 0.033 1538 Dihedral : 6.088 67.191 1331 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.49 % Allowed : 17.82 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.02 (0.25), residues: 1102 helix: 0.95 (0.28), residues: 368 sheet: -0.30 (0.29), residues: 287 loop : -0.50 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.025 0.001 TYR R 284 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.038 Fit side-chains REVERT: B 325 MET cc_start: 0.8750 (tpp) cc_final: 0.8455 (tpt) REVERT: N 93 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8109 (ttp) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 1.2837 time to fit residues: 154.5658 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 227 CYS Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9080 Z= 0.164 Angle : 0.510 7.794 12299 Z= 0.265 Chirality : 0.041 0.138 1391 Planarity : 0.003 0.034 1538 Dihedral : 5.797 65.024 1331 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 18.76 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.12 (0.25), residues: 1102 helix: 1.08 (0.28), residues: 367 sheet: -0.18 (0.30), residues: 273 loop : -0.45 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.014 0.001 PHE R 309 TYR 0.014 0.001 TYR R 313 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.089 Fit side-chains REVERT: B 325 MET cc_start: 0.8722 (tpp) cc_final: 0.8365 (tpt) REVERT: N 93 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: R 73 GLU cc_start: 0.7712 (pm20) cc_final: 0.7227 (pm20) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 1.3190 time to fit residues: 152.1585 Evaluate side-chains 106 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 227 CYS Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9080 Z= 0.137 Angle : 0.504 8.214 12299 Z= 0.260 Chirality : 0.040 0.140 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.494 64.987 1331 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.24 % Allowed : 19.48 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.25 (0.25), residues: 1102 helix: 1.24 (0.28), residues: 367 sheet: -0.12 (0.30), residues: 273 loop : -0.42 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.000 HIS R 280 PHE 0.014 0.001 PHE R 309 TYR 0.023 0.001 TYR R 284 ARG 0.009 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.066 Fit side-chains REVERT: B 325 MET cc_start: 0.8702 (tpp) cc_final: 0.8328 (tpt) REVERT: N 93 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: N 147 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6954 (m) REVERT: R 73 GLU cc_start: 0.7736 (pm20) cc_final: 0.7191 (pm20) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 1.3023 time to fit residues: 151.2781 Evaluate side-chains 102 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088146 restraints weight = 13980.277| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.14 r_work: 0.3109 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9080 Z= 0.170 Angle : 0.531 9.487 12299 Z= 0.273 Chirality : 0.041 0.132 1391 Planarity : 0.003 0.038 1538 Dihedral : 5.768 67.068 1331 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 20.00 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.32 (0.25), residues: 1102 helix: 1.32 (0.28), residues: 367 sheet: -0.04 (0.30), residues: 271 loop : -0.42 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.019 0.001 PHE R 286 TYR 0.014 0.001 TYR R 313 ARG 0.009 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3532.64 seconds wall clock time: 63 minutes 39.39 seconds (3819.39 seconds total)