Starting phenix.real_space_refine on Thu May 1 06:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.map" model { file = "/net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p12_17343/05_2025/8p12_17343.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 77 5.16 5 C 6549 2.51 5 N 1700 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10266 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2530 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain: "A" Number of atoms: 1699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1714 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2416 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 310} Chain: "G" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1699 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "H" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1629 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS A 305 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS A 305 " occ=0.43 Time building chain proxies: 7.07, per 1000 atoms: 0.69 Number of scatterers: 10266 At special positions: 0 Unit cell: (100.1, 115.7, 141.7, 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 77 16.00 O 1940 8.00 N 1700 7.00 C 6549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 2 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 165 " - pdb=" SG CYS H 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 19 sheets defined 32.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'R' and resid 33 through 65 Proline residue: R 53 - end of helix removed outlier: 3.692A pdb=" N LEU R 59 " --> pdb=" O ASN R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 69 Processing helix chain 'R' and resid 70 through 72 No H-bonds generated for 'chain 'R' and resid 70 through 72' Processing helix chain 'R' and resid 73 through 90 Processing helix chain 'R' and resid 90 through 99 Processing helix chain 'R' and resid 105 through 141 Processing helix chain 'R' and resid 149 through 169 Processing helix chain 'R' and resid 199 through 211 Processing helix chain 'R' and resid 212 through 237 Processing helix chain 'R' and resid 240 through 278 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 284 through 290 Processing helix chain 'R' and resid 290 through 297 Processing helix chain 'R' and resid 297 through 307 Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 310 through 317 Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.158A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.597A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.508A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 32 through 48 removed outlier: 3.645A pdb=" N CYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 56 removed outlier: 3.916A pdb=" N LYS G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.550A pdb=" N LEU L 107 " --> pdb=" O ALA L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 Processing helix chain 'L' and resid 206 through 212 Processing helix chain 'H' and resid 105 through 109 Processing sheet with id=AA1, first strand: chain 'R' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'R' and resid 178 through 181 removed outlier: 4.389A pdb=" N SER R 186 " --> pdb=" O GLU R 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.845A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.620A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.650A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.983A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.769A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.788A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.146A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 23 through 26 removed outlier: 3.636A pdb=" N THR L 24 " --> pdb=" O ARG L 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE L 40 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS L 42 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE L 95 " --> pdb=" O CYS L 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.946A pdb=" N GLU L 129 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.946A pdb=" N GLU L 129 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 138 through 142 removed outlier: 3.740A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER L 155 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU L 205 " --> pdb=" O SER L 155 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL L 157 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU L 203 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE L 159 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER L 201 " --> pdb=" O PHE L 159 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN L 161 " --> pdb=" O MET L 199 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N MET L 199 " --> pdb=" O ASN L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 177 through 179 removed outlier: 3.804A pdb=" N TYR L 216 " --> pdb=" O PHE L 233 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE L 233 " --> pdb=" O TYR L 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.887A pdb=" N VAL H 97 " --> pdb=" O CYS H 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.574A pdb=" N THR H 132 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR H 112 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA H 110 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.578A pdb=" N TYR H 147 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H 166 " --> pdb=" O TYR H 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL H 208 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 163 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 169 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR H 200 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU H 199 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU H 195 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR H 201 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA H 193 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER H 203 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 176 through 179 removed outlier: 3.516A pdb=" N ALA H 223 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 231 " --> pdb=" O VAL H 222 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1336 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: 4.01 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 1 1.07 - 1.26: 1671 1.26 - 1.45: 2988 1.45 - 1.64: 5742 1.64 - 1.83: 111 Bond restraints: 10513 Sorted by residual: bond pdb=" CB PRO R 291 " pdb=" CG PRO R 291 " ideal model delta sigma weight residual 1.492 0.879 0.613 5.00e-02 4.00e+02 1.50e+02 bond pdb=" CG PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 1.503 1.214 0.289 3.40e-02 8.65e+02 7.22e+01 bond pdb=" CG PRO G 58 " pdb=" CD PRO G 58 " ideal model delta sigma weight residual 1.503 1.360 0.143 3.40e-02 8.65e+02 1.76e+01 bond pdb=" N PRO R 291 " pdb=" CA PRO R 291 " ideal model delta sigma weight residual 1.471 1.508 -0.037 1.29e-02 6.01e+03 8.06e+00 bond pdb=" C ILE R 290 " pdb=" N PRO R 291 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.08e+00 ... (remaining 10508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.44: 14259 10.44 - 20.89: 10 20.89 - 31.33: 1 31.33 - 41.77: 1 41.77 - 52.21: 1 Bond angle restraints: 14272 Sorted by residual: angle pdb=" N PRO R 291 " pdb=" CD PRO R 291 " pdb=" CG PRO R 291 " ideal model delta sigma weight residual 103.20 77.39 25.81 1.50e+00 4.44e-01 2.96e+02 angle pdb=" CA PRO R 291 " pdb=" CB PRO R 291 " pdb=" CG PRO R 291 " ideal model delta sigma weight residual 104.50 72.93 31.57 1.90e+00 2.77e-01 2.76e+02 angle pdb=" CB PRO R 291 " pdb=" CG PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 106.10 158.31 -52.21 3.20e+00 9.77e-02 2.66e+02 angle pdb=" N PRO G 58 " pdb=" CD PRO G 58 " pdb=" CG PRO G 58 " ideal model delta sigma weight residual 103.20 90.48 12.72 1.50e+00 4.44e-01 7.20e+01 angle pdb=" CA PRO R 291 " pdb=" N PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 112.00 101.02 10.98 1.40e+00 5.10e-01 6.15e+01 ... (remaining 14267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 5533 17.27 - 34.55: 490 34.55 - 51.82: 137 51.82 - 69.09: 26 69.09 - 86.37: 17 Dihedral angle restraints: 6203 sinusoidal: 2396 harmonic: 3807 Sorted by residual: dihedral pdb=" CB CYS H 165 " pdb=" SG CYS H 165 " pdb=" SG CYS H 220 " pdb=" CB CYS H 220 " ideal model delta sinusoidal sigma weight residual -86.00 -147.19 61.19 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" N PRO R 291 " pdb=" CG PRO R 291 " pdb=" CD PRO R 291 " pdb=" CB PRO R 291 " ideal model delta sinusoidal sigma weight residual -30.00 -114.27 84.27 1 1.50e+01 4.44e-03 3.84e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -121.93 35.93 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 6200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1272 0.057 - 0.114: 293 0.114 - 0.171: 22 0.171 - 0.228: 5 0.228 - 0.285: 5 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CB ILE A 343 " pdb=" CA ILE A 343 " pdb=" CG1 ILE A 343 " pdb=" CG2 ILE A 343 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE R 290 " pdb=" N ILE R 290 " pdb=" C ILE R 290 " pdb=" CB ILE R 290 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL R 162 " pdb=" CA VAL R 162 " pdb=" CG1 VAL R 162 " pdb=" CG2 VAL R 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1594 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 312 " -0.030 2.00e-02 2.50e+03 6.02e-02 3.63e+01 pdb=" C GLN R 312 " 0.104 2.00e-02 2.50e+03 pdb=" O GLN R 312 " -0.039 2.00e-02 2.50e+03 pdb=" N PHE R 313 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 311 " -0.025 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C LYS R 311 " 0.084 2.00e-02 2.50e+03 pdb=" O LYS R 311 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN R 312 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 315 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ASN R 315 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN R 315 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS R 316 " -0.019 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 272 2.67 - 3.23: 10317 3.23 - 3.79: 16811 3.79 - 4.34: 22364 4.34 - 4.90: 36180 Nonbonded interactions: 85944 Sorted by model distance: nonbonded pdb=" OG1 THR R 242 " pdb=" OE1 GLU A 318 " model vdw 2.114 3.040 nonbonded pdb=" O TRP A 258 " pdb=" OG1 THR A 262 " model vdw 2.155 3.040 nonbonded pdb=" O TYR L 210 " pdb=" OH TYR L 216 " model vdw 2.217 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.220 3.120 nonbonded pdb=" O TRP R 175 " pdb=" OG SER R 176 " model vdw 2.224 3.040 ... (remaining 85939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 1.170 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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 : 0.008 0.613 10519 Z= 0.237 Angle : 1.109 52.214 14284 Z= 0.593 Chirality : 0.048 0.285 1597 Planarity : 0.006 0.061 1813 Dihedral : 15.144 86.366 3739 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.09 % Allowed : 18.69 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.37 (0.23), residues: 1301 helix: 0.09 (0.26), residues: 360 sheet: 0.60 (0.28), residues: 341 loop : -0.90 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 175 HIS 0.008 0.001 HIS R 211 PHE 0.037 0.002 PHE R 294 TYR 0.019 0.002 TYR R 136 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.16626 ( 474) hydrogen bonds : angle 8.34696 ( 1336) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.03555 ( 12) covalent geometry : bond 0.00769 (10513) covalent geometry : angle 1.10876 (14272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.6853 (ppp) cc_final: 0.6474 (ppp) REVERT: R 86 MET cc_start: 0.3565 (tpt) cc_final: 0.3120 (tpt) REVERT: R 155 MET cc_start: 0.7990 (ttt) cc_final: 0.7366 (ptm) REVERT: A 10 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7191 (mmmt) REVERT: A 354 PHE cc_start: 0.1987 (m-80) cc_final: 0.0459 (p90) REVERT: B 117 LEU cc_start: 0.7212 (mt) cc_final: 0.6579 (pp) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2049 time to fit residues: 33.7172 Evaluate side-chains 93 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 HIS A 256 ASN A 306 GLN B 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.116538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.094620 restraints weight = 92367.993| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 7.05 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10519 Z= 0.196 Angle : 0.718 13.969 14284 Z= 0.373 Chirality : 0.045 0.213 1597 Planarity : 0.005 0.056 1813 Dihedral : 5.078 24.224 1412 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.20 % Allowed : 16.75 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.01 (0.23), residues: 1301 helix: 0.80 (0.26), residues: 368 sheet: 0.49 (0.27), residues: 348 loop : -0.79 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS H 54 PHE 0.022 0.002 PHE R 91 TYR 0.036 0.002 TYR A 302 ARG 0.005 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 474) hydrogen bonds : angle 6.72513 ( 1336) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.95552 ( 12) covalent geometry : bond 0.00434 (10513) covalent geometry : angle 0.71771 (14272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 44 MET cc_start: 0.8987 (tmm) cc_final: 0.8700 (tmm) REVERT: R 91 PHE cc_start: 0.8371 (m-10) cc_final: 0.8126 (m-10) REVERT: R 155 MET cc_start: 0.8047 (ttt) cc_final: 0.7357 (ptt) REVERT: R 181 GLU cc_start: 0.7725 (pp20) cc_final: 0.7387 (pm20) REVERT: R 291 PRO cc_start: 0.7317 (Cg_exo) cc_final: 0.7032 (Cg_endo) REVERT: R 308 MET cc_start: 0.8530 (mmm) cc_final: 0.7391 (tpt) REVERT: R 317 MET cc_start: 0.6774 (ppp) cc_final: 0.6394 (ppp) REVERT: B 117 LEU cc_start: 0.7294 (mt) cc_final: 0.6867 (pp) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.2049 time to fit residues: 35.1422 Evaluate side-chains 113 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 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 = 0.4501 r_free = 0.4501 target = 0.117080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.095557 restraints weight = 79816.618| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 6.53 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10519 Z= 0.143 Angle : 0.645 12.320 14284 Z= 0.330 Chirality : 0.043 0.184 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.755 23.609 1410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.38 % Allowed : 17.11 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.09 (0.23), residues: 1301 helix: 0.94 (0.27), residues: 368 sheet: 0.62 (0.27), residues: 351 loop : -0.83 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE R 91 TYR 0.035 0.001 TYR A 302 ARG 0.003 0.001 ARG L 235 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 474) hydrogen bonds : angle 6.26142 ( 1336) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.87165 ( 12) covalent geometry : bond 0.00317 (10513) covalent geometry : angle 0.64484 (14272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7023 (ppp) cc_final: 0.6654 (ppp) REVERT: R 86 MET cc_start: 0.4366 (tpt) cc_final: 0.4142 (tpp) REVERT: R 155 MET cc_start: 0.8096 (ttt) cc_final: 0.7382 (ptm) REVERT: R 308 MET cc_start: 0.8543 (mmm) cc_final: 0.7253 (tpt) REVERT: B 117 LEU cc_start: 0.7367 (mt) cc_final: 0.6782 (pp) REVERT: G 35 LYS cc_start: 0.8878 (tttt) cc_final: 0.8581 (ttpt) REVERT: L 191 ASP cc_start: 0.7606 (t0) cc_final: 0.7376 (t0) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.2078 time to fit residues: 37.7236 Evaluate side-chains 109 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 195 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.115308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.093988 restraints weight = 71840.968| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 6.08 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10519 Z= 0.210 Angle : 0.691 13.240 14284 Z= 0.356 Chirality : 0.045 0.240 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.997 27.825 1410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.09 % Allowed : 17.46 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.10 (0.23), residues: 1301 helix: 0.84 (0.26), residues: 368 sheet: 0.36 (0.27), residues: 353 loop : -0.88 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.010 0.001 HIS H 54 PHE 0.016 0.002 PHE R 91 TYR 0.034 0.002 TYR A 302 ARG 0.006 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 474) hydrogen bonds : angle 6.25993 ( 1336) SS BOND : bond 0.00151 ( 6) SS BOND : angle 1.06819 ( 12) covalent geometry : bond 0.00465 (10513) covalent geometry : angle 0.69036 (14272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7321 (ppp) cc_final: 0.6995 (ppp) REVERT: R 91 PHE cc_start: 0.8352 (m-10) cc_final: 0.8122 (m-10) REVERT: R 155 MET cc_start: 0.7912 (ttt) cc_final: 0.7055 (ptm) REVERT: R 207 MET cc_start: 0.8695 (mmm) cc_final: 0.8441 (mmm) REVERT: H 160 MET cc_start: 0.8553 (tmm) cc_final: 0.8013 (tmm) REVERT: H 179 TRP cc_start: 0.6562 (m100) cc_final: 0.6204 (m100) outliers start: 35 outliers final: 27 residues processed: 122 average time/residue: 0.2001 time to fit residues: 36.3238 Evaluate side-chains 121 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain R residue 276 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 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 = 0.4495 r_free = 0.4495 target = 0.116388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.096191 restraints weight = 57127.848| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 5.29 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4077 r_free = 0.4077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4077 r_free = 0.4077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10519 Z= 0.142 Angle : 0.666 16.137 14284 Z= 0.332 Chirality : 0.043 0.170 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.784 25.785 1410 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.03 % Allowed : 18.87 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.05 (0.23), residues: 1301 helix: 0.89 (0.27), residues: 368 sheet: 0.38 (0.27), residues: 357 loop : -0.86 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 211 HIS 0.003 0.001 HIS H 54 PHE 0.012 0.001 PHE B 241 TYR 0.032 0.001 TYR A 302 ARG 0.003 0.000 ARG L 235 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 474) hydrogen bonds : angle 6.12972 ( 1336) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.86080 ( 12) covalent geometry : bond 0.00316 (10513) covalent geometry : angle 0.66580 (14272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7404 (ppp) cc_final: 0.7135 (ppp) REVERT: R 155 MET cc_start: 0.8019 (ttt) cc_final: 0.7250 (ptm) REVERT: R 191 TYR cc_start: 0.7301 (p90) cc_final: 0.7075 (p90) REVERT: R 214 ILE cc_start: 0.7956 (mm) cc_final: 0.7696 (mm) REVERT: R 308 MET cc_start: 0.8394 (mmm) cc_final: 0.6872 (tpt) REVERT: R 317 MET cc_start: 0.6069 (ppp) cc_final: 0.5716 (ppp) REVERT: L 191 ASP cc_start: 0.7646 (t0) cc_final: 0.7412 (t0) REVERT: H 160 MET cc_start: 0.8162 (tmm) cc_final: 0.7661 (tmm) outliers start: 23 outliers final: 21 residues processed: 115 average time/residue: 0.1971 time to fit residues: 34.1311 Evaluate side-chains 116 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.114383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.092689 restraints weight = 94578.006| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 7.55 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10519 Z= 0.214 Angle : 0.699 13.743 14284 Z= 0.358 Chirality : 0.045 0.175 1597 Planarity : 0.005 0.051 1813 Dihedral : 5.025 28.285 1410 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.35 % Allowed : 17.99 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.23 (0.23), residues: 1301 helix: 0.75 (0.26), residues: 370 sheet: 0.10 (0.27), residues: 348 loop : -0.84 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.011 0.001 HIS H 54 PHE 0.018 0.002 PHE A 354 TYR 0.031 0.002 TYR A 302 ARG 0.011 0.001 ARG R 21 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 474) hydrogen bonds : angle 6.26848 ( 1336) SS BOND : bond 0.00173 ( 6) SS BOND : angle 1.07697 ( 12) covalent geometry : bond 0.00480 (10513) covalent geometry : angle 0.69815 (14272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7281 (ppp) cc_final: 0.7049 (ppp) REVERT: R 91 PHE cc_start: 0.8397 (m-10) cc_final: 0.8169 (m-10) REVERT: R 155 MET cc_start: 0.7834 (ttt) cc_final: 0.6964 (ptm) REVERT: R 191 TYR cc_start: 0.7658 (p90) cc_final: 0.7437 (p90) REVERT: R 214 ILE cc_start: 0.8208 (mm) cc_final: 0.7979 (mm) REVERT: R 308 MET cc_start: 0.8518 (mmm) cc_final: 0.6913 (tpt) REVERT: R 317 MET cc_start: 0.6216 (ppp) cc_final: 0.5945 (ppp) REVERT: B 54 HIS cc_start: 0.3957 (OUTLIER) cc_final: 0.2727 (m-70) REVERT: G 31 MET cc_start: 0.6257 (ppp) cc_final: 0.5707 (ppp) REVERT: H 160 MET cc_start: 0.8604 (tmm) cc_final: 0.8117 (tmm) outliers start: 38 outliers final: 31 residues processed: 123 average time/residue: 0.2309 time to fit residues: 42.9629 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 0.0000 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.115430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.094076 restraints weight = 85516.521| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 6.71 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10519 Z= 0.126 Angle : 0.663 16.699 14284 Z= 0.329 Chirality : 0.043 0.148 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.707 25.499 1410 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.38 % Allowed : 19.31 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1301 helix: 0.76 (0.26), residues: 374 sheet: 0.15 (0.27), residues: 359 loop : -0.83 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.006 0.001 HIS R 211 PHE 0.013 0.001 PHE B 241 TYR 0.029 0.001 TYR A 302 ARG 0.003 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 474) hydrogen bonds : angle 6.04851 ( 1336) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.75176 ( 12) covalent geometry : bond 0.00281 (10513) covalent geometry : angle 0.66333 (14272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7245 (ppp) cc_final: 0.7037 (ppp) REVERT: R 40 LEU cc_start: 0.9011 (pp) cc_final: 0.8793 (tt) REVERT: R 44 MET cc_start: 0.8768 (ppp) cc_final: 0.8387 (tmm) REVERT: R 191 TYR cc_start: 0.7531 (p90) cc_final: 0.7313 (p90) REVERT: R 214 ILE cc_start: 0.8067 (mm) cc_final: 0.7814 (mm) REVERT: R 238 GLN cc_start: 0.6759 (pm20) cc_final: 0.6518 (pm20) REVERT: R 308 MET cc_start: 0.8509 (mmm) cc_final: 0.7003 (tpt) REVERT: R 317 MET cc_start: 0.6225 (ppp) cc_final: 0.5994 (ppp) REVERT: B 336 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5774 (mp) REVERT: L 191 ASP cc_start: 0.7714 (t0) cc_final: 0.7433 (t0) REVERT: H 160 MET cc_start: 0.8245 (tmm) cc_final: 0.7786 (tmm) REVERT: H 163 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7046 (mm) outliers start: 27 outliers final: 20 residues processed: 118 average time/residue: 0.2295 time to fit residues: 41.0221 Evaluate side-chains 115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.115035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.094545 restraints weight = 63996.477| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 5.61 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10519 Z= 0.144 Angle : 0.660 14.686 14284 Z= 0.331 Chirality : 0.044 0.157 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.714 26.760 1410 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.12 % Allowed : 19.93 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1301 helix: 0.63 (0.26), residues: 374 sheet: 0.15 (0.27), residues: 357 loop : -0.78 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.004 0.001 HIS H 54 PHE 0.016 0.001 PHE R 91 TYR 0.027 0.001 TYR A 302 ARG 0.004 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 474) hydrogen bonds : angle 6.01889 ( 1336) SS BOND : bond 0.00115 ( 6) SS BOND : angle 0.80675 ( 12) covalent geometry : bond 0.00324 (10513) covalent geometry : angle 0.66014 (14272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7153 (ppp) cc_final: 0.6945 (ppp) REVERT: R 44 MET cc_start: 0.8721 (ppp) cc_final: 0.8252 (tmm) REVERT: R 191 TYR cc_start: 0.7511 (p90) cc_final: 0.7307 (p90) REVERT: R 214 ILE cc_start: 0.8112 (mm) cc_final: 0.7864 (mm) REVERT: R 238 GLN cc_start: 0.6765 (pm20) cc_final: 0.6524 (pm20) REVERT: R 308 MET cc_start: 0.8444 (mmm) cc_final: 0.6941 (tpt) REVERT: R 317 MET cc_start: 0.6211 (ppp) cc_final: 0.5979 (ppp) REVERT: B 336 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5815 (mp) REVERT: L 191 ASP cc_start: 0.7720 (t0) cc_final: 0.7462 (t0) REVERT: H 163 LEU cc_start: 0.7664 (mp) cc_final: 0.6901 (mt) outliers start: 24 outliers final: 22 residues processed: 111 average time/residue: 0.1894 time to fit residues: 33.8843 Evaluate side-chains 113 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.093498 restraints weight = 91569.210| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 6.95 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10519 Z= 0.143 Angle : 0.666 14.870 14284 Z= 0.334 Chirality : 0.044 0.219 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.725 26.268 1410 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.20 % Allowed : 20.11 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.23), residues: 1301 helix: 0.62 (0.26), residues: 374 sheet: 0.18 (0.27), residues: 358 loop : -0.76 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.005 0.001 HIS R 211 PHE 0.021 0.001 PHE B 292 TYR 0.027 0.001 TYR A 302 ARG 0.004 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 474) hydrogen bonds : angle 6.00181 ( 1336) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.79043 ( 12) covalent geometry : bond 0.00323 (10513) covalent geometry : angle 0.66633 (14272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7395 (ppp) cc_final: 0.7191 (ppp) REVERT: R 40 LEU cc_start: 0.9227 (tt) cc_final: 0.8858 (pp) REVERT: R 44 MET cc_start: 0.8634 (ppp) cc_final: 0.8092 (tmm) REVERT: R 86 MET cc_start: 0.4637 (tpt) cc_final: 0.3692 (tpt) REVERT: R 191 TYR cc_start: 0.7639 (p90) cc_final: 0.7432 (p90) REVERT: R 214 ILE cc_start: 0.8144 (mm) cc_final: 0.7885 (mm) REVERT: R 238 GLN cc_start: 0.6555 (pm20) cc_final: 0.6249 (pm20) REVERT: R 253 MET cc_start: 0.6371 (ttt) cc_final: 0.6097 (ttt) REVERT: R 308 MET cc_start: 0.8573 (mmm) cc_final: 0.7100 (tpt) REVERT: B 336 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5779 (mp) REVERT: L 191 ASP cc_start: 0.7720 (t0) cc_final: 0.7499 (t0) REVERT: H 160 MET cc_start: 0.8269 (tmm) cc_final: 0.7822 (tmm) REVERT: H 163 LEU cc_start: 0.7984 (mp) cc_final: 0.7257 (mt) outliers start: 25 outliers final: 24 residues processed: 112 average time/residue: 0.2231 time to fit residues: 38.3004 Evaluate side-chains 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.115126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.095762 restraints weight = 52800.218| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 5.66 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10519 Z= 0.138 Angle : 0.673 15.134 14284 Z= 0.338 Chirality : 0.044 0.215 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.697 26.256 1410 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.47 % Allowed : 20.02 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.24), residues: 1301 helix: 0.69 (0.26), residues: 369 sheet: 0.17 (0.28), residues: 355 loop : -0.74 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.006 0.001 HIS R 211 PHE 0.036 0.001 PHE B 292 TYR 0.026 0.001 TYR A 302 ARG 0.003 0.000 ARG L 235 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 474) hydrogen bonds : angle 5.98960 ( 1336) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.75602 ( 12) covalent geometry : bond 0.00312 (10513) covalent geometry : angle 0.67302 (14272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7470 (ppp) cc_final: 0.7245 (ppp) REVERT: R 40 LEU cc_start: 0.9351 (tt) cc_final: 0.8954 (pp) REVERT: R 44 MET cc_start: 0.8767 (ppp) cc_final: 0.8275 (tmm) REVERT: R 191 TYR cc_start: 0.7739 (p90) cc_final: 0.7500 (p90) REVERT: R 207 MET cc_start: 0.8767 (mmm) cc_final: 0.7887 (mmm) REVERT: R 214 ILE cc_start: 0.8176 (mm) cc_final: 0.7920 (mm) REVERT: R 238 GLN cc_start: 0.6497 (pm20) cc_final: 0.6172 (pm20) REVERT: R 253 MET cc_start: 0.6264 (ttt) cc_final: 0.5978 (ttt) REVERT: R 308 MET cc_start: 0.8497 (mmm) cc_final: 0.7398 (tpt) REVERT: R 317 MET cc_start: 0.6924 (ppp) cc_final: 0.6454 (ppp) REVERT: B 336 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5648 (mp) REVERT: G 31 MET cc_start: 0.5313 (ppp) cc_final: 0.4930 (ppp) REVERT: L 191 ASP cc_start: 0.7816 (t0) cc_final: 0.7546 (t0) REVERT: H 160 MET cc_start: 0.8248 (tmm) cc_final: 0.7814 (tmm) REVERT: H 204 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7337 (p) outliers start: 28 outliers final: 26 residues processed: 120 average time/residue: 0.2275 time to fit residues: 43.0240 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 TYR Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.115716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.094174 restraints weight = 92342.498| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 7.01 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10519 Z= 0.126 Angle : 0.674 15.111 14284 Z= 0.334 Chirality : 0.044 0.206 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.599 25.286 1410 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.20 % Allowed : 20.37 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.13 (0.24), residues: 1301 helix: 0.69 (0.26), residues: 369 sheet: 0.20 (0.28), residues: 355 loop : -0.70 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.007 0.001 HIS R 211 PHE 0.028 0.001 PHE B 292 TYR 0.026 0.001 TYR A 302 ARG 0.003 0.000 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 474) hydrogen bonds : angle 5.90709 ( 1336) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.69975 ( 12) covalent geometry : bond 0.00283 (10513) covalent geometry : angle 0.67412 (14272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5760.81 seconds wall clock time: 101 minutes 49.27 seconds (6109.27 seconds total)