Starting phenix.real_space_refine on Sun Dec 29 10:03:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p12_17343/12_2024/8p12_17343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p12_17343/12_2024/8p12_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_17343/12_2024/8p12_17343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p12_17343/12_2024/8p12_17343.map" model { file = "/net/cci-nas-00/data/ceres_data/8p12_17343/12_2024/8p12_17343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p12_17343/12_2024/8p12_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-5532/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: 7.10, 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 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: 1.27 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: 3.36 Time building geometry restraints manager: 2.90 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: 1.990 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.840 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- 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 : 1.362 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: 0.2295 time to fit residues: 37.7147 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 : 1.405 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 44 MET cc_start: 0.8845 (tmm) cc_final: 0.8580 (tmm) REVERT: R 91 PHE cc_start: 0.8194 (m-10) cc_final: 0.7979 (m-10) REVERT: R 155 MET cc_start: 0.8011 (ttt) cc_final: 0.7394 (ptt) REVERT: R 181 GLU cc_start: 0.7618 (pp20) cc_final: 0.7329 (pm20) REVERT: R 291 PRO cc_start: 0.7099 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: R 308 MET cc_start: 0.8513 (mmm) cc_final: 0.7268 (tpt) REVERT: R 317 MET cc_start: 0.6750 (ppp) cc_final: 0.5947 (ppp) REVERT: B 117 LEU cc_start: 0.7180 (mt) cc_final: 0.6812 (pp) outliers start: 25 outliers final: 20 residues processed: 116 average time/residue: 0.2108 time to fit residues: 35.8641 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 : 1.188 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10513 Z= 0.202 Angle : 0.645 12.416 14272 Z= 0.330 Chirality : 0.043 0.183 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.754 23.303 1410 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.38 % Allowed : 17.20 % Favored : 80.42 % 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: 0.94 (0.27), residues: 368 sheet: 0.63 (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 A 57 PHE 0.015 0.001 PHE R 91 TYR 0.035 0.001 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 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.6850 (ppp) cc_final: 0.6450 (ppp) REVERT: R 155 MET cc_start: 0.8064 (ttt) cc_final: 0.7392 (ptm) REVERT: R 308 MET cc_start: 0.8565 (mmm) cc_final: 0.7152 (tpt) REVERT: R 317 MET cc_start: 0.6678 (ppp) cc_final: 0.6285 (ppp) REVERT: B 117 LEU cc_start: 0.7311 (mt) cc_final: 0.6754 (pp) REVERT: G 35 LYS cc_start: 0.8624 (tttt) cc_final: 0.8423 (ttpt) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 0.2098 time to fit residues: 37.4533 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 : 1.207 ------------------------------------------------------------------------------- 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 61 MET 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 115 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1940 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= 0.212 Angle : 0.636 13.804 14272 Z= 0.324 Chirality : 0.043 0.191 1597 Planarity : 0.005 0.051 1813 Dihedral : 4.687 26.161 1410 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.73 % Allowed : 17.02 % Favored : 80.25 % 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: 0.98 (0.27), residues: 368 sheet: 0.54 (0.27), residues: 359 loop : -0.82 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS H 54 PHE 0.013 0.001 PHE R 91 TYR 0.033 0.001 TYR A 302 ARG 0.003 0.000 ARG B 283 *********************** 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: 31 poor density : 99 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.6985 (ppp) cc_final: 0.6652 (ppp) REVERT: R 91 PHE cc_start: 0.8245 (m-10) cc_final: 0.7972 (m-10) REVERT: R 155 MET cc_start: 0.7935 (ttt) cc_final: 0.7217 (ptm) REVERT: B 117 LEU cc_start: 0.7341 (mt) cc_final: 0.6818 (pp) REVERT: B 211 TRP cc_start: 0.6274 (OUTLIER) cc_final: 0.5871 (m100) REVERT: H 160 MET cc_start: 0.8301 (tmm) cc_final: 0.7777 (tmm) outliers start: 31 outliers final: 23 residues processed: 121 average time/residue: 0.2093 time to fit residues: 37.6764 Evaluate side-chains 117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 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 32 LEU Chi-restraints excluded: chain G residue 62 ASN 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 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 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10513 Z= 0.239 Angle : 0.666 16.863 14272 Z= 0.336 Chirality : 0.043 0.163 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.769 26.487 1410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.56 % Allowed : 17.99 % 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: 0.00 (0.23), residues: 1301 helix: 0.98 (0.27), residues: 368 sheet: 0.34 (0.27), residues: 352 loop : -0.80 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 179 HIS 0.005 0.001 HIS H 54 PHE 0.010 0.001 PHE L 159 TYR 0.031 0.002 TYR A 302 ARG 0.003 0.001 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 123 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.7157 (ppp) cc_final: 0.6885 (ppp) REVERT: R 155 MET cc_start: 0.7989 (ttt) cc_final: 0.7253 (ptm) REVERT: R 191 TYR cc_start: 0.7381 (p90) cc_final: 0.7155 (p90) REVERT: R 308 MET cc_start: 0.8460 (mmm) cc_final: 0.6755 (tpt) REVERT: R 317 MET cc_start: 0.6814 (ppp) cc_final: 0.5882 (ppp) REVERT: B 117 LEU cc_start: 0.7291 (mt) cc_final: 0.6877 (pp) REVERT: B 211 TRP cc_start: 0.6311 (OUTLIER) cc_final: 0.5911 (m100) REVERT: L 191 ASP cc_start: 0.7433 (t0) cc_final: 0.7226 (t0) REVERT: H 160 MET cc_start: 0.8261 (tmm) cc_final: 0.7805 (tmm) outliers start: 29 outliers final: 23 residues processed: 115 average time/residue: 0.2189 time to fit residues: 36.8179 Evaluate side-chains 115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10513 Z= 0.295 Angle : 0.678 12.351 14272 Z= 0.348 Chirality : 0.044 0.180 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.939 28.177 1410 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.00 % Allowed : 17.90 % 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: -0.10 (0.23), residues: 1301 helix: 0.89 (0.26), residues: 370 sheet: 0.16 (0.27), residues: 350 loop : -0.77 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.009 0.001 HIS H 54 PHE 0.015 0.002 PHE R 91 TYR 0.030 0.002 TYR A 302 ARG 0.010 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 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: R 1 MET cc_start: 0.6954 (ppp) cc_final: 0.6742 (ppp) REVERT: R 155 MET cc_start: 0.7798 (ttt) cc_final: 0.6994 (ptm) REVERT: R 207 MET cc_start: 0.8269 (mmt) cc_final: 0.8033 (mmm) REVERT: R 214 ILE cc_start: 0.7992 (mm) cc_final: 0.7715 (mm) REVERT: G 31 MET cc_start: 0.6087 (ppp) cc_final: 0.5685 (ppp) REVERT: H 160 MET cc_start: 0.8511 (tmm) cc_final: 0.8098 (tmm) outliers start: 34 outliers final: 27 residues processed: 122 average time/residue: 0.1928 time to fit residues: 35.7731 Evaluate side-chains 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 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 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 119 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10513 Z= 0.193 Angle : 0.641 15.113 14272 Z= 0.327 Chirality : 0.043 0.160 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.752 26.872 1410 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.29 % Allowed : 19.14 % Favored : 78.57 % 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: 0.84 (0.26), residues: 369 sheet: 0.20 (0.27), residues: 359 loop : -0.80 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 211 HIS 0.003 0.001 HIS H 54 PHE 0.039 0.001 PHE B 292 TYR 0.029 0.001 TYR A 302 ARG 0.003 0.000 ARG R 21 *********************** 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 121 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9257 (tt) cc_final: 0.8851 (pp) REVERT: R 44 MET cc_start: 0.8671 (ppp) cc_final: 0.8299 (tmm) REVERT: R 86 MET cc_start: 0.5296 (tpp) cc_final: 0.4768 (tpp) REVERT: R 207 MET cc_start: 0.8335 (mmt) cc_final: 0.8060 (mmm) REVERT: R 214 ILE cc_start: 0.7985 (mm) cc_final: 0.7726 (mm) REVERT: R 308 MET cc_start: 0.8231 (mmm) cc_final: 0.6827 (tpt) REVERT: R 317 MET cc_start: 0.6660 (ppp) cc_final: 0.5760 (ppp) REVERT: B 336 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6144 (mp) REVERT: G 31 MET cc_start: 0.5881 (ppp) cc_final: 0.5370 (ppp) REVERT: L 191 ASP cc_start: 0.7614 (t0) cc_final: 0.7396 (t0) REVERT: H 160 MET cc_start: 0.8245 (tmm) cc_final: 0.7884 (tmm) outliers start: 26 outliers final: 21 residues processed: 113 average time/residue: 0.2064 time to fit residues: 35.4008 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 : 1.201 ------------------------------------------------------------------------------- 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 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 277 SER Chi-restraints excluded: chain B residue 336 LEU 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 43 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 84 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10513 Z= 0.181 Angle : 0.648 15.052 14272 Z= 0.327 Chirality : 0.043 0.159 1597 Planarity : 0.005 0.050 1813 Dihedral : 4.627 26.982 1410 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.03 % Allowed : 19.05 % Favored : 78.92 % 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: 0.77 (0.26), residues: 369 sheet: 0.21 (0.27), residues: 361 loop : -0.71 (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 B 54 PHE 0.035 0.001 PHE B 292 TYR 0.027 0.001 TYR A 302 ARG 0.003 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 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9190 (tt) cc_final: 0.8845 (pp) REVERT: R 44 MET cc_start: 0.8594 (ppp) cc_final: 0.8191 (tmm) REVERT: R 86 MET cc_start: 0.5274 (tpp) cc_final: 0.4583 (tpp) REVERT: R 207 MET cc_start: 0.8519 (mmt) cc_final: 0.8230 (mmm) REVERT: R 214 ILE cc_start: 0.7972 (mm) cc_final: 0.7703 (mm) REVERT: R 308 MET cc_start: 0.8358 (mmm) cc_final: 0.7018 (tpt) REVERT: R 317 MET cc_start: 0.6458 (ppp) cc_final: 0.5467 (ppp) REVERT: B 336 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5969 (mp) REVERT: G 31 MET cc_start: 0.5966 (ppp) cc_final: 0.5534 (ppp) REVERT: L 191 ASP cc_start: 0.7589 (t0) cc_final: 0.7332 (t0) REVERT: H 160 MET cc_start: 0.8224 (tmm) cc_final: 0.7882 (tmm) outliers start: 23 outliers final: 20 residues processed: 116 average time/residue: 0.1819 time to fit residues: 32.7581 Evaluate side-chains 112 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 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 B residue 336 LEU 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 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 118 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10513 Z= 0.201 Angle : 0.642 15.061 14272 Z= 0.326 Chirality : 0.044 0.212 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.630 27.019 1410 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.20 % Allowed : 19.22 % Favored : 78.57 % 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 (0.24), residues: 1301 helix: 0.78 (0.26), residues: 370 sheet: 0.22 (0.28), residues: 360 loop : -0.73 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.005 0.001 HIS H 54 PHE 0.024 0.001 PHE R 91 TYR 0.027 0.001 TYR A 302 ARG 0.003 0.000 ARG B 197 *********************** 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 : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9206 (tt) cc_final: 0.8900 (pp) REVERT: R 44 MET cc_start: 0.8600 (ppp) cc_final: 0.8205 (tmm) REVERT: R 86 MET cc_start: 0.5337 (tpp) cc_final: 0.5009 (tpp) REVERT: R 214 ILE cc_start: 0.7994 (mm) cc_final: 0.7725 (mm) REVERT: R 253 MET cc_start: 0.6238 (ttt) cc_final: 0.5974 (ttt) REVERT: R 308 MET cc_start: 0.8358 (mmm) cc_final: 0.6897 (tpt) REVERT: R 317 MET cc_start: 0.6473 (ppp) cc_final: 0.5713 (ppp) REVERT: B 336 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5972 (mp) REVERT: L 191 ASP cc_start: 0.7622 (t0) cc_final: 0.7411 (t0) outliers start: 25 outliers final: 22 residues processed: 111 average time/residue: 0.1769 time to fit residues: 30.7363 Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 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 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 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 74 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 244 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10513 Z= 0.235 Angle : 0.681 15.084 14272 Z= 0.343 Chirality : 0.044 0.220 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.734 28.025 1410 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.38 % Allowed : 19.40 % Favored : 78.22 % 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: -0.16 (0.23), residues: 1301 helix: 0.67 (0.26), residues: 370 sheet: 0.23 (0.28), residues: 353 loop : -0.76 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.007 0.001 HIS H 54 PHE 0.024 0.001 PHE R 91 TYR 0.026 0.002 TYR A 302 ARG 0.005 0.000 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 119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: R 40 LEU cc_start: 0.9204 (tt) cc_final: 0.8871 (pp) REVERT: R 44 MET cc_start: 0.8617 (ppp) cc_final: 0.8249 (tmm) REVERT: R 86 MET cc_start: 0.5284 (tpp) cc_final: 0.5072 (tpp) REVERT: R 155 MET cc_start: 0.7767 (ttt) cc_final: 0.6982 (ptm) REVERT: R 214 ILE cc_start: 0.8101 (mm) cc_final: 0.7839 (mm) REVERT: R 238 GLN cc_start: 0.6887 (pm20) cc_final: 0.6624 (pm20) REVERT: R 253 MET cc_start: 0.6301 (ttt) cc_final: 0.6015 (ttt) REVERT: R 308 MET cc_start: 0.8270 (mmm) cc_final: 0.6847 (tpt) REVERT: R 317 MET cc_start: 0.6507 (ppp) cc_final: 0.5792 (ppp) REVERT: B 336 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5988 (mp) REVERT: G 31 MET cc_start: 0.5376 (ppp) cc_final: 0.5119 (ptm) outliers start: 27 outliers final: 23 residues processed: 113 average time/residue: 0.1800 time to fit residues: 31.8080 Evaluate side-chains 114 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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 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 31 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.115332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.093842 restraints weight = 69519.143| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 6.04 r_work (final): 0.4025 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10513 Z= 0.270 Angle : 0.703 15.039 14272 Z= 0.357 Chirality : 0.045 0.206 1597 Planarity : 0.005 0.049 1813 Dihedral : 4.915 28.296 1410 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.12 % Allowed : 19.40 % Favored : 78.48 % 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: -0.27 (0.23), residues: 1301 helix: 0.54 (0.26), residues: 375 sheet: 0.19 (0.28), residues: 328 loop : -0.79 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.010 0.001 HIS H 54 PHE 0.025 0.002 PHE B 292 TYR 0.030 0.002 TYR A 302 ARG 0.004 0.001 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.26 seconds wall clock time: 41 minutes 5.77 seconds (2465.77 seconds total)