Starting phenix.real_space_refine on Fri Feb 14 14:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p12_17343/02_2025/8p12_17343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p12_17343/02_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_17343/02_2025/8p12_17343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p12_17343/02_2025/8p12_17343.map" model { file = "/net/cci-nas-00/data/ceres_data/8p12_17343/02_2025/8p12_17343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p12_17343/02_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-5592/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: 6.66, per 1000 atoms: 0.65 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: 2.44 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: 1.32 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: 3.15 Time building geometry restraints manager: 2.89 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: 1.540 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: 0.070 Set scattering table: 0.110 Process input model: 26.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- 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 10513 Z= 0.607 Angle : 1.109 52.214 14272 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 *********************** 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 : 1.222 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: 0.2122 time to fit residues: 34.8136 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 : 1.141 ------------------------------------------------------------------------------- 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 = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.094621 restraints weight = 92362.413| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 7.04 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10513 Z= 0.282 Angle : 0.718 13.964 14272 Z= 0.374 Chirality : 0.045 0.213 1597 Planarity : 0.005 0.056 1813 Dihedral : 5.078 24.171 1412 Min Nonbonded Distance : 2.503 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 *********************** 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 : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 44 MET cc_start: 0.8988 (tmm) cc_final: 0.8699 (tmm) REVERT: R 91 PHE cc_start: 0.8373 (m-10) cc_final: 0.8128 (m-10) REVERT: R 155 MET cc_start: 0.8047 (ttt) cc_final: 0.7357 (ptt) REVERT: R 181 GLU cc_start: 0.7726 (pp20) cc_final: 0.7388 (pm20) REVERT: R 291 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.7030 (Cg_endo) REVERT: R 308 MET cc_start: 0.8529 (mmm) cc_final: 0.7389 (tpt) REVERT: R 317 MET cc_start: 0.6775 (ppp) cc_final: 0.6393 (ppp) REVERT: B 117 LEU cc_start: 0.7294 (mt) cc_final: 0.6866 (pp) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.2133 time to fit residues: 36.5258 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 : 1.152 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 59 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.116916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.095367 restraints weight = 79498.700| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 6.56 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10513 Z= 0.215 Angle : 0.650 12.262 14272 Z= 0.333 Chirality : 0.043 0.183 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.789 23.630 1410 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.38 % Allowed : 17.46 % Favored : 80.16 % 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: 0.06 (0.23), residues: 1301 helix: 0.93 (0.27), residues: 368 sheet: 0.59 (0.27), residues: 351 loop : -0.85 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS A 57 PHE 0.014 0.001 PHE R 91 TYR 0.036 0.002 TYR A 302 ARG 0.003 0.001 ARG L 132 *********************** 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 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7057 (ppp) cc_final: 0.6687 (ppp) REVERT: R 155 MET cc_start: 0.8071 (ttt) cc_final: 0.7373 (ptm) REVERT: R 308 MET cc_start: 0.8592 (mmm) cc_final: 0.7288 (tpt) REVERT: B 117 LEU cc_start: 0.7426 (mt) cc_final: 0.6915 (pp) REVERT: G 35 LYS cc_start: 0.8947 (tttt) cc_final: 0.8635 (ttpt) REVERT: L 191 ASP cc_start: 0.7629 (t0) cc_final: 0.7385 (t0) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 0.2121 time to fit residues: 39.0918 Evaluate side-chains 107 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 7 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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** ** B 340 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.117706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.096608 restraints weight = 70988.204| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 6.16 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10513 Z= 0.175 Angle : 0.625 14.079 14272 Z= 0.316 Chirality : 0.043 0.164 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.591 24.735 1410 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.94 % Allowed : 17.72 % Favored : 80.34 % 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: 0.16 (0.23), residues: 1301 helix: 1.01 (0.27), residues: 368 sheet: 0.63 (0.27), residues: 359 loop : -0.80 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS A 57 PHE 0.011 0.001 PHE R 91 TYR 0.035 0.001 TYR A 302 ARG 0.002 0.000 ARG L 235 *********************** 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 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7089 (ppp) cc_final: 0.6790 (ppp) REVERT: R 91 PHE cc_start: 0.8477 (m-10) cc_final: 0.8171 (m-10) REVERT: R 155 MET cc_start: 0.8076 (ttt) cc_final: 0.7368 (ptm) REVERT: B 117 LEU cc_start: 0.7347 (mt) cc_final: 0.6834 (pp) REVERT: B 211 TRP cc_start: 0.6139 (OUTLIER) cc_final: 0.5707 (m100) outliers start: 22 outliers final: 17 residues processed: 117 average time/residue: 0.2062 time to fit residues: 36.0677 Evaluate side-chains 110 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain B residue 211 TRP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 113 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.116921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.097657 restraints weight = 57419.031| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 5.82 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10513 Z= 0.214 Angle : 0.653 15.465 14272 Z= 0.327 Chirality : 0.043 0.179 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.628 26.138 1410 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.56 % Allowed : 18.08 % Favored : 79.37 % 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: 0.11 (0.23), residues: 1301 helix: 1.03 (0.27), residues: 368 sheet: 0.45 (0.27), residues: 364 loop : -0.76 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS H 54 PHE 0.011 0.001 PHE L 159 TYR 0.035 0.001 TYR A 302 ARG 0.003 0.000 ARG A 15 *********************** 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 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: R 1 MET cc_start: 0.7323 (ppp) cc_final: 0.7044 (ppp) REVERT: R 155 MET cc_start: 0.8031 (ttt) cc_final: 0.7299 (ptm) REVERT: R 181 GLU cc_start: 0.7530 (pp20) cc_final: 0.6964 (pm20) REVERT: R 308 MET cc_start: 0.8423 (mmm) cc_final: 0.6873 (tpt) REVERT: R 317 MET cc_start: 0.6335 (ppp) cc_final: 0.5863 (ppp) REVERT: A 198 MET cc_start: 0.4890 (mmp) cc_final: 0.3943 (ptp) REVERT: B 117 LEU cc_start: 0.7241 (mt) cc_final: 0.6776 (pp) REVERT: B 211 TRP cc_start: 0.6261 (OUTLIER) cc_final: 0.5867 (m100) REVERT: L 191 ASP cc_start: 0.7649 (t0) cc_final: 0.7351 (t0) REVERT: H 101 MET cc_start: 0.7341 (ttt) cc_final: 0.7046 (ttt) REVERT: H 160 MET cc_start: 0.8337 (tmm) cc_final: 0.7764 (tmm) REVERT: H 179 TRP cc_start: 0.6481 (m100) cc_final: 0.6239 (m100) outliers start: 29 outliers final: 23 residues processed: 115 average time/residue: 0.1984 time to fit residues: 34.1240 Evaluate side-chains 113 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 61 MET 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 211 TRP 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 62 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 1.5302 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.114792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.093284 restraints weight = 94714.115| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 7.53 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 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 = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10513 Z= 0.301 Angle : 0.698 12.544 14272 Z= 0.356 Chirality : 0.045 0.179 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.951 28.301 1410 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.65 % Allowed : 17.81 % Favored : 79.54 % 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: 0.81 (0.26), residues: 374 sheet: 0.19 (0.27), residues: 350 loop : -0.75 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.011 0.001 HIS H 54 PHE 0.015 0.002 PHE R 91 TYR 0.033 0.002 TYR A 302 ARG 0.006 0.001 ARG R 21 *********************** 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 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: R 1 MET cc_start: 0.7648 (ppp) cc_final: 0.7321 (ppp) REVERT: R 155 MET cc_start: 0.7817 (ttt) cc_final: 0.6964 (ptm) REVERT: R 191 TYR cc_start: 0.7533 (p90) cc_final: 0.7313 (p90) REVERT: R 214 ILE cc_start: 0.8129 (mm) cc_final: 0.7885 (mm) REVERT: R 308 MET cc_start: 0.8477 (mmm) cc_final: 0.6880 (tpt) REVERT: R 317 MET cc_start: 0.6639 (ppp) cc_final: 0.6118 (ppp) REVERT: G 31 MET cc_start: 0.6299 (tmm) cc_final: 0.5906 (ppp) REVERT: H 101 MET cc_start: 0.7448 (ttt) cc_final: 0.7051 (ttt) REVERT: H 160 MET cc_start: 0.8535 (tmm) cc_final: 0.8052 (tmm) REVERT: H 179 TRP cc_start: 0.6593 (m100) cc_final: 0.6274 (m100) outliers start: 30 outliers final: 26 residues processed: 117 average time/residue: 0.2207 time to fit residues: 38.1760 Evaluate side-chains 117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 126 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.116687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.095020 restraints weight = 86822.105| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 7.49 r_work (final): 0.4044 ------------------------------------------------------------------------------- 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 = 0.36 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10513 Z= 0.189 Angle : 0.656 16.555 14272 Z= 0.329 Chirality : 0.043 0.152 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.746 26.840 1410 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.12 % Allowed : 19.22 % 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: -0.08 (0.23), residues: 1301 helix: 0.84 (0.27), residues: 374 sheet: 0.17 (0.27), residues: 361 loop : -0.71 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 211 HIS 0.003 0.001 HIS H 54 PHE 0.035 0.001 PHE B 292 TYR 0.031 0.001 TYR A 302 ARG 0.003 0.000 ARG L 235 *********************** 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 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 MET cc_start: 0.8865 (ppp) cc_final: 0.8559 (tmm) REVERT: R 86 MET cc_start: 0.4776 (tpp) cc_final: 0.4295 (tpp) REVERT: R 91 PHE cc_start: 0.8115 (m-10) cc_final: 0.7889 (m-10) REVERT: R 214 ILE cc_start: 0.8056 (mm) cc_final: 0.7808 (mm) REVERT: R 308 MET cc_start: 0.8581 (mmm) cc_final: 0.7192 (tpt) REVERT: R 317 MET cc_start: 0.6678 (ppp) cc_final: 0.6194 (ppp) REVERT: L 191 ASP cc_start: 0.7879 (t0) cc_final: 0.7522 (t0) REVERT: H 101 MET cc_start: 0.7393 (ttt) cc_final: 0.7032 (ttt) REVERT: H 160 MET cc_start: 0.8483 (tmm) cc_final: 0.7965 (tmm) REVERT: H 179 TRP cc_start: 0.6608 (m100) cc_final: 0.6289 (m100) outliers start: 24 outliers final: 21 residues processed: 114 average time/residue: 0.1991 time to fit residues: 34.0356 Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL 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 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 256 ARG Chi-restraints excluded: chain B residue 277 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.116002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.095744 restraints weight = 64373.601| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 5.70 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10513 Z= 0.183 Angle : 0.657 14.659 14272 Z= 0.325 Chirality : 0.043 0.152 1597 Planarity : 0.004 0.050 1813 Dihedral : 4.620 27.028 1410 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.12 % Allowed : 19.05 % Favored : 78.84 % 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: -0.03 (0.24), residues: 1301 helix: 0.84 (0.27), residues: 369 sheet: 0.20 (0.27), residues: 361 loop : -0.65 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS R 211 PHE 0.040 0.001 PHE B 292 TYR 0.031 0.001 TYR A 302 ARG 0.004 0.000 ARG A 15 *********************** 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 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9205 (tt) cc_final: 0.8860 (pp) REVERT: R 44 MET cc_start: 0.8688 (ppp) cc_final: 0.8290 (tmm) REVERT: R 86 MET cc_start: 0.4967 (tpp) cc_final: 0.4366 (tpp) REVERT: R 207 MET cc_start: 0.8583 (mmm) cc_final: 0.8065 (mmm) REVERT: R 214 ILE cc_start: 0.8017 (mm) cc_final: 0.7758 (mm) REVERT: R 308 MET cc_start: 0.8453 (mmm) cc_final: 0.7051 (tpt) REVERT: R 317 MET cc_start: 0.6628 (ppp) cc_final: 0.6219 (ppp) REVERT: L 191 ASP cc_start: 0.7645 (t0) cc_final: 0.7399 (t0) REVERT: H 101 MET cc_start: 0.7377 (ttt) cc_final: 0.7033 (ttt) REVERT: H 160 MET cc_start: 0.8376 (tmm) cc_final: 0.7986 (tmm) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.1876 time to fit residues: 33.7538 Evaluate side-chains 111 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.114036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.092218 restraints weight = 90932.124| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 6.94 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10513 Z= 0.278 Angle : 0.696 14.699 14272 Z= 0.352 Chirality : 0.045 0.217 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.864 27.896 1410 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.47 % Allowed : 19.58 % 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: -0.16 (0.23), residues: 1301 helix: 0.75 (0.26), residues: 369 sheet: 0.05 (0.27), residues: 352 loop : -0.67 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 179 HIS 0.009 0.001 HIS H 54 PHE 0.025 0.002 PHE R 91 TYR 0.032 0.002 TYR A 302 ARG 0.004 0.001 ARG B 256 *********************** 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 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.192 Fit side-chains REVERT: R 40 LEU cc_start: 0.9250 (tt) cc_final: 0.8946 (pp) REVERT: R 44 MET cc_start: 0.8763 (ppp) cc_final: 0.8241 (tmm) REVERT: R 86 MET cc_start: 0.4825 (tpp) cc_final: 0.4220 (tpp) REVERT: R 91 PHE cc_start: 0.7874 (m-10) cc_final: 0.7662 (m-10) REVERT: R 155 MET cc_start: 0.7844 (ttt) cc_final: 0.7008 (ptm) REVERT: R 214 ILE cc_start: 0.8174 (mm) cc_final: 0.7922 (mm) REVERT: R 253 MET cc_start: 0.6420 (ttt) cc_final: 0.6177 (ttt) REVERT: R 308 MET cc_start: 0.8595 (mmm) cc_final: 0.6933 (tpt) REVERT: L 191 ASP cc_start: 0.7811 (t0) cc_final: 0.7468 (t0) REVERT: H 101 MET cc_start: 0.7632 (ttt) cc_final: 0.7220 (ttt) REVERT: H 160 MET cc_start: 0.8577 (tmm) cc_final: 0.8372 (tmm) outliers start: 28 outliers final: 25 residues processed: 111 average time/residue: 0.1767 time to fit residues: 30.5810 Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL 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 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 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 140 LYS 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: 2.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.095620 restraints weight = 52542.343| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 5.44 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10513 Z= 0.222 Angle : 0.695 15.026 14272 Z= 0.347 Chirality : 0.044 0.215 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.780 27.239 1410 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.03 % Allowed : 20.02 % 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: -0.21 (0.24), residues: 1301 helix: 0.60 (0.26), residues: 375 sheet: 0.15 (0.28), residues: 354 loop : -0.75 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 179 HIS 0.005 0.001 HIS H 54 PHE 0.024 0.001 PHE B 292 TYR 0.028 0.001 TYR A 302 ARG 0.004 0.001 ARG A 15 ********************** 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 116 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9334 (tt) cc_final: 0.9117 (tp) REVERT: R 44 MET cc_start: 0.8709 (ppp) cc_final: 0.8265 (tmm) REVERT: R 86 MET cc_start: 0.4737 (tpp) cc_final: 0.4126 (tpp) REVERT: R 91 PHE cc_start: 0.7773 (m-10) cc_final: 0.7545 (m-10) REVERT: R 214 ILE cc_start: 0.8158 (mm) cc_final: 0.7895 (mm) REVERT: R 253 MET cc_start: 0.6332 (ttt) cc_final: 0.6069 (ttt) REVERT: R 308 MET cc_start: 0.8477 (mmm) cc_final: 0.7177 (tpt) REVERT: A 10 LYS cc_start: 0.7496 (mmtt) cc_final: 0.6936 (mmmt) REVERT: L 191 ASP cc_start: 0.7814 (t0) cc_final: 0.7419 (t0) REVERT: H 101 MET cc_start: 0.7400 (ttt) cc_final: 0.7043 (ttt) REVERT: H 160 MET cc_start: 0.8540 (tmm) cc_final: 0.8192 (tmm) outliers start: 23 outliers final: 22 residues processed: 109 average time/residue: 0.1768 time to fit residues: 30.0327 Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain B residue 61 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.117239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.095638 restraints weight = 92272.351| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 7.88 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10513 Z= 0.181 Angle : 0.669 15.111 14272 Z= 0.334 Chirality : 0.044 0.217 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.629 26.610 1410 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.85 % Allowed : 20.28 % Favored : 77.87 % 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: -0.15 (0.24), residues: 1301 helix: 0.63 (0.27), residues: 369 sheet: 0.22 (0.28), residues: 355 loop : -0.71 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.007 0.001 HIS R 211 PHE 0.023 0.001 PHE B 292 TYR 0.029 0.001 TYR A 302 ARG 0.005 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5160.55 seconds wall clock time: 92 minutes 40.59 seconds (5560.59 seconds total)