Starting phenix.real_space_refine on Mon Dec 30 00:15:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.map" model { file = "/net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rua_24701/12_2024/7rua_24701.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7350 2.51 5 N 1992 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 11603 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1947 SG CYS A 283 54.502 65.935 97.337 1.00 99.40 S ATOM 1970 SG CYS A 286 55.392 68.382 94.693 1.00 92.44 S Restraints were copied for chains: B, F, G, H Time building chain proxies: 8.34, per 1000 atoms: 0.72 Number of scatterers: 11603 At special positions: 0 Unit cell: (108.075, 136.125, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2188 8.00 N 1992 7.00 C 7350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.39 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 286 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 283 " pdb="ZN ZN A 403 " - pdb=" SG CYS B 283 " Number of angles added : 6 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 2 sheets defined 71.4% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.534A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 116 through 133 removed outlier: 4.177A pdb=" N MET A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 Processing helix chain 'A' and resid 163 through 187 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.382A pdb=" N LYS A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 245 through 263 Processing helix chain 'A' and resid 283 through 304 Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.546A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.534A pdb=" N ALA B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 116 through 133 removed outlier: 4.178A pdb=" N MET B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 163 through 187 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 211 through 232 removed outlier: 4.383A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 245 through 263 Processing helix chain 'B' and resid 283 through 304 Processing helix chain 'B' and resid 321 through 334 removed outlier: 3.546A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.619A pdb=" N GLN C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 Processing helix chain 'C' and resid 58 through 76 Processing helix chain 'C' and resid 78 through 97 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 133 removed outlier: 4.382A pdb=" N VAL C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 157 removed outlier: 3.739A pdb=" N HIS C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 191 through 206 removed outlier: 3.821A pdb=" N VAL C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 234 through 250 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'D' and resid 1009 through 1014 removed outlier: 4.320A pdb=" N ALA D1013 " --> pdb=" O PRO D1009 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D1014 " --> pdb=" O TRP D1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1014' Processing helix chain 'D' and resid 1015 through 1017 No H-bonds generated for 'chain 'D' and resid 1015 through 1017' Processing helix chain 'D' and resid 1018 through 1032 removed outlier: 3.535A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D1031 " --> pdb=" O GLN D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'D' and resid 1062 through 1075 Processing helix chain 'D' and resid 1081 through 1088 Processing helix chain 'D' and resid 1092 through 1113 removed outlier: 4.199A pdb=" N TYR D1098 " --> pdb=" O VAL D1094 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.619A pdb=" N GLN F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 56 Processing helix chain 'F' and resid 58 through 76 Processing helix chain 'F' and resid 78 through 97 Processing helix chain 'F' and resid 101 through 115 Processing helix chain 'F' and resid 119 through 133 removed outlier: 4.381A pdb=" N VAL F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 157 removed outlier: 3.738A pdb=" N HIS F 146 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.821A pdb=" N VAL F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 234 through 250 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 284 Processing helix chain 'G' and resid 1009 through 1014 removed outlier: 4.320A pdb=" N ALA G1013 " --> pdb=" O PRO G1009 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G1014 " --> pdb=" O TRP G1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1009 through 1014' Processing helix chain 'G' and resid 1015 through 1017 No H-bonds generated for 'chain 'G' and resid 1015 through 1017' Processing helix chain 'G' and resid 1018 through 1032 removed outlier: 3.534A pdb=" N GLN G1023 " --> pdb=" O VAL G1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS G1031 " --> pdb=" O GLN G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1039 through 1044 Processing helix chain 'G' and resid 1057 through 1070 Processing helix chain 'G' and resid 1076 through 1083 Processing helix chain 'G' and resid 1087 through 1108 removed outlier: 4.199A pdb=" N TYR G1093 " --> pdb=" O VAL G1089 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 129 Processing helix chain 'H' and resid 131 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.533A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N MET A 97 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 64 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 63 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP A 160 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 65 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 34 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN A 268 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 240 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 269 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 312 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 271 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.534A pdb=" N VAL B 62 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N MET B 97 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 64 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 63 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASP B 160 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 65 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 34 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE B 243 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 240 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 269 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 312 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 271 " --> pdb=" O LEU B 312 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2148 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: 3.44 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3821 1.34 - 1.46: 2330 1.46 - 1.58: 5577 1.58 - 1.70: 10 1.70 - 1.82: 106 Bond restraints: 11844 Sorted by residual: bond pdb=" CA VAL D1019 " pdb=" CB VAL D1019 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 7.45e-01 bond pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.20e-02 6.94e+03 6.72e-01 bond pdb=" CD ARG D1030 " pdb=" NE ARG D1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CD ARG G1030 " pdb=" NE ARG G1030 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.40e-02 5.10e+03 6.67e-01 bond pdb=" CA VAL G1019 " pdb=" CB VAL G1019 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.44e-01 ... (remaining 11839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 15519 1.34 - 2.68: 372 2.68 - 4.02: 99 4.02 - 5.36: 22 5.36 - 6.70: 8 Bond angle restraints: 16020 Sorted by residual: angle pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH2 ARG A 224 " ideal model delta sigma weight residual 119.20 121.62 -2.42 9.00e-01 1.23e+00 7.22e+00 angle pdb=" NE ARG B 224 " pdb=" CZ ARG B 224 " pdb=" NH2 ARG B 224 " ideal model delta sigma weight residual 119.20 121.59 -2.39 9.00e-01 1.23e+00 7.07e+00 angle pdb=" C ARG G1094 " pdb=" N GLN G1095 " pdb=" CA GLN G1095 " ideal model delta sigma weight residual 120.72 116.53 4.19 1.67e+00 3.59e-01 6.30e+00 angle pdb=" C ARG D1099 " pdb=" N GLN D1100 " pdb=" CA GLN D1100 " ideal model delta sigma weight residual 120.72 116.54 4.18 1.67e+00 3.59e-01 6.27e+00 angle pdb=" C1' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" O2' ATP B 401 " ideal model delta sigma weight residual 110.58 103.88 6.70 2.79e+00 1.28e-01 5.76e+00 ... (remaining 16015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6480 17.58 - 35.15: 648 35.15 - 52.73: 136 52.73 - 70.31: 34 70.31 - 87.89: 12 Dihedral angle restraints: 7310 sinusoidal: 3072 harmonic: 4238 Sorted by residual: dihedral pdb=" CA SER F 137 " pdb=" C SER F 137 " pdb=" N GLY F 138 " pdb=" CA GLY F 138 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER C 137 " pdb=" C SER C 137 " pdb=" N GLY C 138 " pdb=" CA GLY C 138 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CD ARG A 224 " pdb=" NE ARG A 224 " pdb=" CZ ARG A 224 " pdb=" NH1 ARG A 224 " ideal model delta sinusoidal sigma weight residual 0.00 -26.87 26.87 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 7307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1568 0.059 - 0.118: 184 0.118 - 0.177: 8 0.177 - 0.236: 2 0.236 - 0.295: 4 Chirality restraints: 1766 Sorted by residual: chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP B 401 " pdb=" C1' ATP B 401 " pdb=" C3' ATP B 401 " pdb=" O2' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" C4' ATP A 401 " pdb=" O3' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1763 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " -0.444 9.50e-02 1.11e+02 1.99e-01 2.51e+01 pdb=" NE ARG A 224 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 224 " 0.443 9.50e-02 1.11e+02 1.99e-01 2.50e+01 pdb=" NE ARG B 224 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 224 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 224 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 224 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G1051 " -0.186 9.50e-02 1.11e+02 8.36e-02 4.41e+00 pdb=" NE ARG G1051 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G1051 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G1051 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G1051 " -0.005 2.00e-02 2.50e+03 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 103 2.52 - 3.11: 9791 3.11 - 3.71: 19541 3.71 - 4.30: 26422 4.30 - 4.90: 43337 Nonbonded interactions: 99194 Sorted by model distance: nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.920 2.170 nonbonded pdb=" O2G ATP B 401 " pdb="MG MG B 402 " model vdw 1.921 2.170 nonbonded pdb=" OE1 GLU A 245 " pdb=" O3' ATP B 401 " model vdw 1.944 3.040 nonbonded pdb=" OE1 GLU B 245 " pdb=" O3' ATP A 401 " model vdw 1.946 3.040 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 402 " model vdw 1.962 2.170 ... (remaining 99189 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 339 or resid 401 through 402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.840 Find NCS groups from input model: 0.450 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11844 Z= 0.213 Angle : 0.566 6.704 16020 Z= 0.293 Chirality : 0.040 0.295 1766 Planarity : 0.008 0.199 2072 Dihedral : 14.914 87.887 4550 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1424 helix: 1.68 (0.17), residues: 944 sheet: 0.12 (0.61), residues: 82 loop : 0.34 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 96 HIS 0.007 0.001 HIS C 43 PHE 0.009 0.001 PHE B 328 TYR 0.011 0.001 TYR A 250 ARG 0.016 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.2998 (mmt) cc_final: 0.2411 (mmm) REVERT: A 121 MET cc_start: 0.1612 (mtt) cc_final: 0.1220 (ptt) REVERT: A 126 MET cc_start: 0.4497 (ttt) cc_final: 0.4143 (tmm) REVERT: A 281 ARG cc_start: 0.6460 (ptm160) cc_final: 0.6199 (ptp-170) REVERT: A 287 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7441 (mt-10) REVERT: B 89 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7539 (mtmt) REVERT: B 118 MET cc_start: 0.3322 (mmt) cc_final: 0.2716 (mmm) REVERT: B 121 MET cc_start: 0.1677 (mtt) cc_final: 0.1408 (ptt) REVERT: B 126 MET cc_start: 0.4622 (ttt) cc_final: 0.4197 (tmm) REVERT: B 281 ARG cc_start: 0.6445 (ptm160) cc_final: 0.6182 (ptp-170) REVERT: B 287 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7434 (mt-10) REVERT: C 27 GLU cc_start: 0.7266 (tt0) cc_final: 0.6905 (mt-10) REVERT: C 36 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7983 (ttpt) REVERT: C 66 MET cc_start: 0.8502 (mmm) cc_final: 0.8278 (mmm) REVERT: C 128 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7123 (mtp180) REVERT: C 238 ASN cc_start: 0.7991 (m-40) cc_final: 0.7717 (m110) REVERT: C 258 LEU cc_start: 0.7103 (mm) cc_final: 0.6882 (mt) REVERT: D 1042 TYR cc_start: 0.7344 (t80) cc_final: 0.7133 (t80) REVERT: F 27 GLU cc_start: 0.7259 (tt0) cc_final: 0.6905 (mt-10) REVERT: F 36 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7993 (ttpt) REVERT: F 66 MET cc_start: 0.8500 (mmm) cc_final: 0.8259 (mmp) REVERT: F 128 ARG cc_start: 0.7408 (mmm-85) cc_final: 0.7116 (mtp180) REVERT: F 238 ASN cc_start: 0.8020 (m-40) cc_final: 0.7734 (m110) REVERT: F 255 PHE cc_start: 0.8342 (t80) cc_final: 0.8094 (t80) REVERT: F 260 GLU cc_start: 0.8140 (tp30) cc_final: 0.7830 (tm-30) REVERT: G 1042 TYR cc_start: 0.7279 (t80) cc_final: 0.6991 (t80) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2552 time to fit residues: 94.0337 Evaluate side-chains 182 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1027 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11844 Z= 0.243 Angle : 0.617 10.446 16020 Z= 0.317 Chirality : 0.041 0.145 1766 Planarity : 0.005 0.055 2072 Dihedral : 7.860 75.819 1630 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.57 % Allowed : 8.78 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.23), residues: 1424 helix: 1.96 (0.17), residues: 976 sheet: -0.18 (0.60), residues: 74 loop : 0.36 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 96 HIS 0.006 0.002 HIS E 106 PHE 0.022 0.002 PHE C 232 TYR 0.024 0.002 TYR C 272 ARG 0.006 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.305 Fit side-chains REVERT: A 89 LYS cc_start: 0.8466 (tptt) cc_final: 0.7806 (mtmt) REVERT: A 118 MET cc_start: 0.3178 (mmt) cc_final: 0.2628 (mpp) REVERT: A 121 MET cc_start: 0.1731 (mtt) cc_final: 0.1218 (ptt) REVERT: A 126 MET cc_start: 0.5379 (ttt) cc_final: 0.4406 (tmm) REVERT: A 128 GLU cc_start: 0.7806 (mm-30) cc_final: 0.6928 (pt0) REVERT: A 281 ARG cc_start: 0.6640 (ptm160) cc_final: 0.6388 (ptp-170) REVERT: B 83 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7811 (mmmt) REVERT: B 89 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7651 (mttt) REVERT: B 118 MET cc_start: 0.3337 (mmt) cc_final: 0.2876 (mpp) REVERT: B 121 MET cc_start: 0.2112 (mtt) cc_final: 0.1675 (ptt) REVERT: B 126 MET cc_start: 0.5244 (ttt) cc_final: 0.4251 (tmm) REVERT: B 179 ARG cc_start: 0.6690 (mtm110) cc_final: 0.6293 (ttt-90) REVERT: B 281 ARG cc_start: 0.6633 (ptm160) cc_final: 0.6394 (ptp-170) REVERT: C 27 GLU cc_start: 0.7168 (tt0) cc_final: 0.6910 (mt-10) REVERT: C 66 MET cc_start: 0.8493 (mmm) cc_final: 0.8193 (mmm) REVERT: C 128 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7371 (mtp180) REVERT: C 208 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8285 (t0) REVERT: C 238 ASN cc_start: 0.8008 (m-40) cc_final: 0.7209 (m110) REVERT: C 271 MET cc_start: 0.6372 (mtt) cc_final: 0.5948 (mmp) REVERT: D 1042 TYR cc_start: 0.7453 (t80) cc_final: 0.7105 (t80) REVERT: F 27 GLU cc_start: 0.7150 (tt0) cc_final: 0.6924 (mt-10) REVERT: F 66 MET cc_start: 0.8495 (mmm) cc_final: 0.8186 (mmm) REVERT: F 128 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7366 (mtp180) REVERT: F 208 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8221 (t0) REVERT: F 238 ASN cc_start: 0.7970 (m-40) cc_final: 0.7148 (m110) REVERT: F 255 PHE cc_start: 0.8351 (t80) cc_final: 0.8042 (t80) REVERT: F 271 MET cc_start: 0.6529 (mtt) cc_final: 0.6077 (mmp) REVERT: G 1042 TYR cc_start: 0.7365 (t80) cc_final: 0.7059 (t80) outliers start: 20 outliers final: 9 residues processed: 203 average time/residue: 0.2556 time to fit residues: 73.9196 Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 1028 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 0.0010 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11844 Z= 0.265 Angle : 0.569 6.412 16020 Z= 0.297 Chirality : 0.041 0.156 1766 Planarity : 0.005 0.057 2072 Dihedral : 7.531 81.185 1630 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.72 % Allowed : 10.89 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.22), residues: 1424 helix: 1.89 (0.16), residues: 976 sheet: -0.82 (0.56), residues: 76 loop : 0.24 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 241 HIS 0.005 0.001 HIS E 106 PHE 0.014 0.001 PHE B 328 TYR 0.028 0.002 TYR C 272 ARG 0.005 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.351 Fit side-chains REVERT: A 89 LYS cc_start: 0.8490 (tptt) cc_final: 0.7876 (mtmt) REVERT: A 118 MET cc_start: 0.3088 (mmt) cc_final: 0.2510 (mpp) REVERT: A 121 MET cc_start: 0.1789 (mtt) cc_final: 0.1311 (ptt) REVERT: A 126 MET cc_start: 0.5328 (ttt) cc_final: 0.4604 (tmm) REVERT: A 128 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6958 (pt0) REVERT: A 157 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7860 (t) REVERT: B 78 ASP cc_start: 0.7967 (t0) cc_final: 0.7586 (m-30) REVERT: B 89 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7756 (mtmt) REVERT: B 118 MET cc_start: 0.3144 (mmt) cc_final: 0.2621 (mpp) REVERT: B 121 MET cc_start: 0.1773 (mtt) cc_final: 0.1382 (ptt) REVERT: B 126 MET cc_start: 0.5393 (ttt) cc_final: 0.4558 (tmm) REVERT: B 128 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6874 (pt0) REVERT: B 179 ARG cc_start: 0.6736 (mtm110) cc_final: 0.6281 (ttt-90) REVERT: B 281 ARG cc_start: 0.6808 (ptm160) cc_final: 0.6599 (ptp-170) REVERT: C 27 GLU cc_start: 0.7191 (tt0) cc_final: 0.6868 (mt-10) REVERT: C 66 MET cc_start: 0.8495 (mmm) cc_final: 0.8255 (mmm) REVERT: C 103 GLU cc_start: 0.7295 (pm20) cc_final: 0.7021 (pm20) REVERT: C 128 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.7311 (mtp180) REVERT: C 208 ASN cc_start: 0.8451 (t0) cc_final: 0.8217 (t0) REVERT: C 238 ASN cc_start: 0.8034 (m-40) cc_final: 0.7124 (m110) REVERT: C 260 GLU cc_start: 0.7873 (tp30) cc_final: 0.7540 (tm-30) REVERT: C 271 MET cc_start: 0.6331 (mtt) cc_final: 0.6067 (mmp) REVERT: C 277 ASP cc_start: 0.8172 (t70) cc_final: 0.7774 (t0) REVERT: D 1024 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6290 (tp-100) REVERT: D 1042 TYR cc_start: 0.7417 (t80) cc_final: 0.7074 (t80) REVERT: F 27 GLU cc_start: 0.7182 (tt0) cc_final: 0.6876 (mt-10) REVERT: F 66 MET cc_start: 0.8509 (mmm) cc_final: 0.8264 (mmm) REVERT: F 103 GLU cc_start: 0.7255 (pm20) cc_final: 0.6983 (pm20) REVERT: F 128 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7361 (mtp180) REVERT: F 208 ASN cc_start: 0.8420 (t0) cc_final: 0.8159 (t0) REVERT: F 238 ASN cc_start: 0.8030 (m-40) cc_final: 0.7105 (m110) REVERT: F 251 LYS cc_start: 0.6720 (mptt) cc_final: 0.6499 (mmtp) REVERT: F 255 PHE cc_start: 0.8405 (t80) cc_final: 0.8150 (t80) REVERT: F 271 MET cc_start: 0.6494 (mtt) cc_final: 0.6214 (mmp) REVERT: F 277 ASP cc_start: 0.8176 (t70) cc_final: 0.7816 (t0) REVERT: G 1026 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7812 (tp) outliers start: 22 outliers final: 17 residues processed: 186 average time/residue: 0.2487 time to fit residues: 65.8310 Evaluate side-chains 176 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 1026 ILE Chi-restraints excluded: chain G residue 1044 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 2.9990 chunk 97 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 299 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1024 GLN G1027 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11844 Z= 0.280 Angle : 0.584 11.650 16020 Z= 0.299 Chirality : 0.041 0.142 1766 Planarity : 0.005 0.062 2072 Dihedral : 7.376 86.485 1630 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 10.97 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1424 helix: 1.82 (0.16), residues: 976 sheet: -1.28 (0.51), residues: 78 loop : 0.07 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 241 HIS 0.004 0.001 HIS C 165 PHE 0.021 0.001 PHE C 255 TYR 0.030 0.002 TYR C 272 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.515 Fit side-chains REVERT: A 78 ASP cc_start: 0.8022 (t0) cc_final: 0.7603 (m-30) REVERT: A 89 LYS cc_start: 0.8483 (tptt) cc_final: 0.7878 (mtmt) REVERT: A 118 MET cc_start: 0.3023 (mmt) cc_final: 0.2418 (mpp) REVERT: A 121 MET cc_start: 0.1890 (mtt) cc_final: 0.1365 (ptt) REVERT: A 126 MET cc_start: 0.5523 (ttt) cc_final: 0.4671 (tmm) REVERT: A 128 GLU cc_start: 0.7719 (mm-30) cc_final: 0.6899 (pt0) REVERT: A 306 ASP cc_start: 0.7186 (t70) cc_final: 0.6684 (m-30) REVERT: B 78 ASP cc_start: 0.8015 (t0) cc_final: 0.7597 (m-30) REVERT: B 89 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7722 (mttt) REVERT: B 118 MET cc_start: 0.3099 (mmt) cc_final: 0.2517 (mpp) REVERT: B 121 MET cc_start: 0.1873 (mtt) cc_final: 0.1432 (ptt) REVERT: B 126 MET cc_start: 0.5494 (ttt) cc_final: 0.4508 (tmm) REVERT: B 128 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6914 (pt0) REVERT: B 179 ARG cc_start: 0.6786 (mtm110) cc_final: 0.6301 (ttt-90) REVERT: B 306 ASP cc_start: 0.7211 (t70) cc_final: 0.6722 (m-30) REVERT: C 27 GLU cc_start: 0.7299 (tt0) cc_final: 0.6880 (mt-10) REVERT: C 103 GLU cc_start: 0.7295 (pm20) cc_final: 0.6979 (pm20) REVERT: C 128 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.7292 (mtp180) REVERT: C 208 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8191 (t0) REVERT: C 238 ASN cc_start: 0.8085 (m-40) cc_final: 0.7156 (m110) REVERT: C 244 LEU cc_start: 0.8482 (mp) cc_final: 0.8047 (mp) REVERT: C 260 GLU cc_start: 0.7916 (tp30) cc_final: 0.7584 (tm-30) REVERT: C 271 MET cc_start: 0.6609 (mtt) cc_final: 0.6187 (mmp) REVERT: C 277 ASP cc_start: 0.8164 (t70) cc_final: 0.7781 (t0) REVERT: D 1024 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6255 (tp-100) REVERT: D 1042 TYR cc_start: 0.7515 (t80) cc_final: 0.7139 (t80) REVERT: F 27 GLU cc_start: 0.7278 (tt0) cc_final: 0.6871 (mt-10) REVERT: F 87 MET cc_start: 0.8333 (mmm) cc_final: 0.7982 (mmm) REVERT: F 103 GLU cc_start: 0.7255 (pm20) cc_final: 0.6936 (pm20) REVERT: F 112 PHE cc_start: 0.8727 (t80) cc_final: 0.8465 (t80) REVERT: F 128 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7256 (mtp180) REVERT: F 161 GLU cc_start: 0.7961 (mp0) cc_final: 0.7707 (mp0) REVERT: F 208 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8146 (t0) REVERT: F 238 ASN cc_start: 0.8087 (m-40) cc_final: 0.7128 (m110) REVERT: F 251 LYS cc_start: 0.6668 (mptt) cc_final: 0.6427 (mmtp) REVERT: F 255 PHE cc_start: 0.8413 (t80) cc_final: 0.8129 (t80) REVERT: F 271 MET cc_start: 0.6495 (mtt) cc_final: 0.6220 (mmp) REVERT: F 277 ASP cc_start: 0.8212 (t70) cc_final: 0.7869 (t0) REVERT: G 1026 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7786 (tp) outliers start: 32 outliers final: 20 residues processed: 184 average time/residue: 0.2538 time to fit residues: 66.6564 Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 1026 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 40.0000 chunk 0 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11844 Z= 0.289 Angle : 0.564 6.582 16020 Z= 0.294 Chirality : 0.041 0.143 1766 Planarity : 0.005 0.062 2072 Dihedral : 7.187 88.831 1630 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.98 % Allowed : 10.42 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.22), residues: 1424 helix: 1.79 (0.16), residues: 976 sheet: -1.52 (0.49), residues: 76 loop : -0.02 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 241 HIS 0.004 0.001 HIS F 165 PHE 0.016 0.001 PHE C 255 TYR 0.023 0.002 TYR C 272 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7892 (t0) cc_final: 0.7502 (m-30) REVERT: A 89 LYS cc_start: 0.8446 (tptt) cc_final: 0.7847 (mtmt) REVERT: A 118 MET cc_start: 0.2972 (mmt) cc_final: 0.2245 (mpp) REVERT: A 121 MET cc_start: 0.1877 (mtt) cc_final: 0.1338 (ptt) REVERT: A 126 MET cc_start: 0.5734 (ttt) cc_final: 0.4869 (tmm) REVERT: A 306 ASP cc_start: 0.7187 (t70) cc_final: 0.6703 (m-30) REVERT: B 78 ASP cc_start: 0.7890 (t0) cc_final: 0.7472 (m-30) REVERT: B 89 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7731 (mttt) REVERT: B 118 MET cc_start: 0.3126 (mmt) cc_final: 0.2435 (mpp) REVERT: B 121 MET cc_start: 0.2037 (mtt) cc_final: 0.1533 (ptt) REVERT: B 126 MET cc_start: 0.5543 (ttt) cc_final: 0.4724 (tmm) REVERT: B 128 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6887 (pt0) REVERT: B 179 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6328 (ttt-90) REVERT: B 306 ASP cc_start: 0.7126 (t70) cc_final: 0.6745 (m-30) REVERT: C 27 GLU cc_start: 0.7369 (tt0) cc_final: 0.6899 (mt-10) REVERT: C 161 GLU cc_start: 0.7909 (mp0) cc_final: 0.7668 (mp0) REVERT: C 208 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8224 (t0) REVERT: C 238 ASN cc_start: 0.8076 (m-40) cc_final: 0.7124 (m110) REVERT: C 260 GLU cc_start: 0.7882 (tp30) cc_final: 0.7480 (tm-30) REVERT: C 271 MET cc_start: 0.6428 (mtt) cc_final: 0.6028 (mmp) REVERT: C 277 ASP cc_start: 0.8190 (t70) cc_final: 0.7813 (t0) REVERT: D 1024 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6289 (tp-100) REVERT: D 1042 TYR cc_start: 0.7578 (t80) cc_final: 0.7122 (t80) REVERT: F 27 GLU cc_start: 0.7352 (tt0) cc_final: 0.6845 (mt-10) REVERT: F 103 GLU cc_start: 0.7254 (pm20) cc_final: 0.6921 (pm20) REVERT: F 161 GLU cc_start: 0.7940 (mp0) cc_final: 0.7686 (mp0) REVERT: F 208 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8158 (t0) REVERT: F 238 ASN cc_start: 0.8133 (m-40) cc_final: 0.7154 (m110) REVERT: F 251 LYS cc_start: 0.6741 (mptt) cc_final: 0.6484 (mmtp) REVERT: F 255 PHE cc_start: 0.8397 (t80) cc_final: 0.8098 (t80) REVERT: F 271 MET cc_start: 0.6536 (mtt) cc_final: 0.6166 (mmp) REVERT: F 277 ASP cc_start: 0.8177 (t70) cc_final: 0.7855 (t0) outliers start: 38 outliers final: 24 residues processed: 196 average time/residue: 0.2195 time to fit residues: 63.5047 Evaluate side-chains 184 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 1023 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11844 Z= 0.273 Angle : 0.574 13.001 16020 Z= 0.295 Chirality : 0.041 0.154 1766 Planarity : 0.005 0.063 2072 Dihedral : 7.029 85.357 1630 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.74 % Allowed : 11.52 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1424 helix: 1.79 (0.17), residues: 976 sheet: -1.90 (0.45), residues: 88 loop : 0.03 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 241 HIS 0.005 0.001 HIS B 308 PHE 0.024 0.001 PHE F 112 TYR 0.024 0.002 TYR C 272 ARG 0.005 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7902 (t0) cc_final: 0.7482 (m-30) REVERT: A 89 LYS cc_start: 0.8419 (tptt) cc_final: 0.7807 (mtmt) REVERT: A 118 MET cc_start: 0.2764 (mmt) cc_final: 0.2028 (mpp) REVERT: A 121 MET cc_start: 0.1989 (mtt) cc_final: 0.1390 (ptt) REVERT: A 126 MET cc_start: 0.5741 (ttt) cc_final: 0.4872 (tmm) REVERT: A 306 ASP cc_start: 0.7186 (t70) cc_final: 0.6805 (m-30) REVERT: B 78 ASP cc_start: 0.7870 (t0) cc_final: 0.7442 (m-30) REVERT: B 89 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7740 (mtmt) REVERT: B 118 MET cc_start: 0.3009 (mmt) cc_final: 0.2280 (mpp) REVERT: B 121 MET cc_start: 0.2140 (mtt) cc_final: 0.1596 (ptt) REVERT: B 126 MET cc_start: 0.5668 (ttt) cc_final: 0.4846 (tmm) REVERT: B 128 GLU cc_start: 0.7741 (mm-30) cc_final: 0.6901 (pt0) REVERT: B 152 MET cc_start: 0.6295 (tmm) cc_final: 0.6061 (tpt) REVERT: B 179 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6320 (ttt-90) REVERT: B 306 ASP cc_start: 0.7135 (t70) cc_final: 0.6828 (m-30) REVERT: C 27 GLU cc_start: 0.7332 (tt0) cc_final: 0.6823 (mt-10) REVERT: C 103 GLU cc_start: 0.7276 (pm20) cc_final: 0.7018 (pm20) REVERT: C 161 GLU cc_start: 0.7910 (mp0) cc_final: 0.7668 (mp0) REVERT: C 208 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8222 (t0) REVERT: C 238 ASN cc_start: 0.8091 (m-40) cc_final: 0.7132 (m110) REVERT: C 241 TRP cc_start: 0.8449 (t60) cc_final: 0.8179 (t60) REVERT: C 260 GLU cc_start: 0.7842 (tp30) cc_final: 0.7435 (tm-30) REVERT: C 271 MET cc_start: 0.6475 (mtt) cc_final: 0.6082 (mmp) REVERT: C 277 ASP cc_start: 0.8139 (t70) cc_final: 0.7758 (t0) REVERT: D 1024 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6315 (tp-100) REVERT: D 1042 TYR cc_start: 0.7597 (t80) cc_final: 0.7192 (t80) REVERT: F 27 GLU cc_start: 0.7330 (tt0) cc_final: 0.6824 (mt-10) REVERT: F 103 GLU cc_start: 0.7269 (pm20) cc_final: 0.6937 (pm20) REVERT: F 161 GLU cc_start: 0.7908 (mp0) cc_final: 0.7652 (mp0) REVERT: F 208 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8163 (t0) REVERT: F 238 ASN cc_start: 0.8174 (m-40) cc_final: 0.7135 (m110) REVERT: F 251 LYS cc_start: 0.6831 (mptt) cc_final: 0.6549 (mmtp) REVERT: F 255 PHE cc_start: 0.8407 (t80) cc_final: 0.8096 (t80) REVERT: F 271 MET cc_start: 0.6552 (mtt) cc_final: 0.6175 (mmp) REVERT: F 277 ASP cc_start: 0.8178 (t70) cc_final: 0.7854 (t0) outliers start: 35 outliers final: 26 residues processed: 180 average time/residue: 0.2250 time to fit residues: 60.0861 Evaluate side-chains 181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1024 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11844 Z= 0.278 Angle : 0.591 18.281 16020 Z= 0.299 Chirality : 0.041 0.164 1766 Planarity : 0.005 0.063 2072 Dihedral : 6.953 83.901 1630 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.98 % Allowed : 12.15 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1424 helix: 1.80 (0.17), residues: 976 sheet: -1.88 (0.45), residues: 86 loop : -0.03 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 241 HIS 0.006 0.001 HIS B 308 PHE 0.021 0.001 PHE C 255 TYR 0.020 0.002 TYR C 272 ARG 0.004 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7899 (t0) cc_final: 0.7467 (m-30) REVERT: A 89 LYS cc_start: 0.8439 (tptt) cc_final: 0.7837 (mtmt) REVERT: A 118 MET cc_start: 0.2711 (mmt) cc_final: 0.1861 (mpp) REVERT: A 121 MET cc_start: 0.2027 (mtt) cc_final: 0.1473 (ptt) REVERT: A 126 MET cc_start: 0.5792 (ttt) cc_final: 0.4948 (tmm) REVERT: A 306 ASP cc_start: 0.7233 (t70) cc_final: 0.6852 (m-30) REVERT: B 78 ASP cc_start: 0.7871 (t0) cc_final: 0.7432 (m-30) REVERT: B 89 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7724 (mtmt) REVERT: B 118 MET cc_start: 0.2954 (mmt) cc_final: 0.2223 (mpp) REVERT: B 121 MET cc_start: 0.2079 (mtt) cc_final: 0.1526 (ptt) REVERT: B 126 MET cc_start: 0.5689 (ttt) cc_final: 0.4888 (tmm) REVERT: B 128 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6845 (pt0) REVERT: B 179 ARG cc_start: 0.6823 (mtm110) cc_final: 0.6295 (ttt-90) REVERT: B 306 ASP cc_start: 0.7139 (t70) cc_final: 0.6814 (m-30) REVERT: C 27 GLU cc_start: 0.7346 (tt0) cc_final: 0.6847 (mt-10) REVERT: C 103 GLU cc_start: 0.7264 (pm20) cc_final: 0.6947 (pm20) REVERT: C 161 GLU cc_start: 0.7910 (mp0) cc_final: 0.7665 (mp0) REVERT: C 208 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (t0) REVERT: C 238 ASN cc_start: 0.8065 (m-40) cc_final: 0.7097 (m110) REVERT: C 260 GLU cc_start: 0.7865 (tp30) cc_final: 0.7453 (tm-30) REVERT: C 277 ASP cc_start: 0.8142 (t70) cc_final: 0.7800 (t0) REVERT: D 1024 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6325 (tp-100) REVERT: D 1042 TYR cc_start: 0.7587 (t80) cc_final: 0.7156 (t80) REVERT: F 27 GLU cc_start: 0.7331 (tt0) cc_final: 0.6798 (mt-10) REVERT: F 103 GLU cc_start: 0.7277 (pm20) cc_final: 0.6958 (pm20) REVERT: F 161 GLU cc_start: 0.7906 (mp0) cc_final: 0.7648 (mp0) REVERT: F 208 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (t0) REVERT: F 238 ASN cc_start: 0.8177 (m-40) cc_final: 0.7119 (m110) REVERT: F 251 LYS cc_start: 0.6852 (mptt) cc_final: 0.6567 (mmtp) REVERT: F 260 GLU cc_start: 0.7865 (tp30) cc_final: 0.7504 (tm-30) REVERT: F 277 ASP cc_start: 0.8173 (t70) cc_final: 0.7862 (t0) outliers start: 38 outliers final: 31 residues processed: 187 average time/residue: 0.2170 time to fit residues: 60.5347 Evaluate side-chains 185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 261 GLN G1024 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11844 Z= 0.206 Angle : 0.568 19.168 16020 Z= 0.286 Chirality : 0.039 0.151 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.707 77.598 1630 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.66 % Allowed : 12.46 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1424 helix: 1.88 (0.17), residues: 980 sheet: -1.99 (0.45), residues: 88 loop : 0.03 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 241 HIS 0.006 0.001 HIS C 43 PHE 0.027 0.001 PHE C 255 TYR 0.019 0.002 TYR F 272 ARG 0.004 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7853 (t0) cc_final: 0.7494 (m-30) REVERT: A 89 LYS cc_start: 0.8403 (tptt) cc_final: 0.7792 (mtmt) REVERT: A 118 MET cc_start: 0.2760 (mmt) cc_final: 0.1904 (mpp) REVERT: A 121 MET cc_start: 0.2006 (mtt) cc_final: 0.1514 (ptt) REVERT: A 126 MET cc_start: 0.5758 (ttt) cc_final: 0.4918 (tmm) REVERT: A 157 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7802 (t) REVERT: A 306 ASP cc_start: 0.7181 (t70) cc_final: 0.6770 (m-30) REVERT: B 78 ASP cc_start: 0.7849 (t0) cc_final: 0.7456 (m-30) REVERT: B 89 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7714 (mtmt) REVERT: B 118 MET cc_start: 0.2910 (mmt) cc_final: 0.2079 (mpp) REVERT: B 121 MET cc_start: 0.2064 (mtt) cc_final: 0.1556 (ptt) REVERT: B 126 MET cc_start: 0.5686 (ttt) cc_final: 0.4910 (tmm) REVERT: B 128 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6788 (pt0) REVERT: C 103 GLU cc_start: 0.7255 (pm20) cc_final: 0.6950 (pm20) REVERT: C 161 GLU cc_start: 0.7878 (mp0) cc_final: 0.7633 (mp0) REVERT: C 208 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8136 (t0) REVERT: C 238 ASN cc_start: 0.8059 (m-40) cc_final: 0.7108 (m110) REVERT: C 241 TRP cc_start: 0.8438 (t60) cc_final: 0.8169 (t60) REVERT: C 277 ASP cc_start: 0.8104 (t70) cc_final: 0.7797 (t0) REVERT: D 1024 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6335 (tp-100) REVERT: F 161 GLU cc_start: 0.7867 (mp0) cc_final: 0.7618 (mp0) REVERT: F 208 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8138 (t0) REVERT: F 238 ASN cc_start: 0.8154 (m-40) cc_final: 0.7102 (m110) REVERT: F 251 LYS cc_start: 0.6803 (mptt) cc_final: 0.6515 (mmtp) REVERT: F 260 GLU cc_start: 0.7797 (tp30) cc_final: 0.7441 (tm-30) REVERT: F 277 ASP cc_start: 0.8122 (t70) cc_final: 0.7854 (t0) outliers start: 34 outliers final: 26 residues processed: 190 average time/residue: 0.2009 time to fit residues: 57.5730 Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 261 GLN Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 131 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN G1024 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11844 Z= 0.222 Angle : 0.597 19.371 16020 Z= 0.296 Chirality : 0.040 0.164 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.648 76.446 1630 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.66 % Allowed : 13.01 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1424 helix: 1.88 (0.17), residues: 976 sheet: -1.95 (0.45), residues: 88 loop : -0.04 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 241 HIS 0.004 0.001 HIS C 43 PHE 0.030 0.001 PHE C 255 TYR 0.022 0.002 TYR F 272 ARG 0.006 0.000 ARG F 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7848 (t0) cc_final: 0.7488 (m-30) REVERT: A 89 LYS cc_start: 0.8407 (tptt) cc_final: 0.7804 (mtmt) REVERT: A 118 MET cc_start: 0.2811 (mmt) cc_final: 0.1918 (mpp) REVERT: A 121 MET cc_start: 0.1986 (mtt) cc_final: 0.1543 (ptt) REVERT: A 126 MET cc_start: 0.5753 (ttt) cc_final: 0.4961 (tmm) REVERT: A 306 ASP cc_start: 0.7090 (t70) cc_final: 0.6777 (m-30) REVERT: B 78 ASP cc_start: 0.7828 (t0) cc_final: 0.7446 (m-30) REVERT: B 89 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7714 (mtmt) REVERT: B 118 MET cc_start: 0.2816 (mmt) cc_final: 0.1957 (mpp) REVERT: B 121 MET cc_start: 0.2111 (mtt) cc_final: 0.1627 (ptt) REVERT: B 126 MET cc_start: 0.5727 (ttt) cc_final: 0.4922 (tmm) REVERT: B 128 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6780 (pt0) REVERT: C 103 GLU cc_start: 0.7256 (pm20) cc_final: 0.6949 (pm20) REVERT: C 161 GLU cc_start: 0.7906 (mp0) cc_final: 0.7661 (mp0) REVERT: C 208 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (t0) REVERT: C 238 ASN cc_start: 0.8070 (m-40) cc_final: 0.7082 (m110) REVERT: C 277 ASP cc_start: 0.8092 (t70) cc_final: 0.7801 (t0) REVERT: D 1024 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6341 (tp-100) REVERT: F 103 GLU cc_start: 0.7181 (pm20) cc_final: 0.6918 (pm20) REVERT: F 161 GLU cc_start: 0.7888 (mp0) cc_final: 0.7637 (mp0) REVERT: F 208 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8109 (t0) REVERT: F 230 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.6873 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8161 (m-40) cc_final: 0.7066 (m110) REVERT: F 251 LYS cc_start: 0.6943 (mptt) cc_final: 0.6635 (mmtp) REVERT: F 277 ASP cc_start: 0.8130 (t70) cc_final: 0.7871 (t0) outliers start: 34 outliers final: 30 residues processed: 182 average time/residue: 0.2034 time to fit residues: 56.0715 Evaluate side-chains 187 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11844 Z= 0.291 Angle : 0.620 19.748 16020 Z= 0.309 Chirality : 0.041 0.163 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.699 78.686 1630 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.98 % Allowed : 13.09 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1424 helix: 1.82 (0.17), residues: 976 sheet: -1.97 (0.45), residues: 88 loop : -0.08 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 241 HIS 0.005 0.001 HIS B 308 PHE 0.029 0.002 PHE C 255 TYR 0.021 0.002 TYR C 272 ARG 0.005 0.000 ARG F 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7841 (t0) cc_final: 0.7443 (m-30) REVERT: A 89 LYS cc_start: 0.8415 (tptt) cc_final: 0.7816 (mtmt) REVERT: A 118 MET cc_start: 0.2749 (mmt) cc_final: 0.1853 (mpp) REVERT: A 121 MET cc_start: 0.2085 (mtt) cc_final: 0.1631 (ptt) REVERT: A 126 MET cc_start: 0.5813 (ttt) cc_final: 0.5030 (tmm) REVERT: A 306 ASP cc_start: 0.7145 (t70) cc_final: 0.6820 (m-30) REVERT: B 78 ASP cc_start: 0.7833 (t0) cc_final: 0.7428 (m-30) REVERT: B 89 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7727 (mtmt) REVERT: B 118 MET cc_start: 0.2805 (mmt) cc_final: 0.1954 (mpp) REVERT: B 121 MET cc_start: 0.2131 (mtt) cc_final: 0.1648 (ptt) REVERT: B 126 MET cc_start: 0.5789 (ttt) cc_final: 0.4981 (tmm) REVERT: B 179 ARG cc_start: 0.6752 (mtm110) cc_final: 0.6230 (ttt-90) REVERT: C 161 GLU cc_start: 0.7915 (mp0) cc_final: 0.7669 (mp0) REVERT: C 208 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8147 (t0) REVERT: C 238 ASN cc_start: 0.8105 (m-40) cc_final: 0.7138 (m110) REVERT: C 241 TRP cc_start: 0.8400 (t60) cc_final: 0.8152 (t60) REVERT: C 277 ASP cc_start: 0.8092 (t70) cc_final: 0.7812 (t0) REVERT: D 1024 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6352 (tp-100) REVERT: F 103 GLU cc_start: 0.7241 (pm20) cc_final: 0.7016 (pm20) REVERT: F 161 GLU cc_start: 0.7883 (mp0) cc_final: 0.7621 (mp0) REVERT: F 208 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (t0) REVERT: F 230 PRO cc_start: 0.7365 (Cg_exo) cc_final: 0.6992 (Cg_endo) REVERT: F 238 ASN cc_start: 0.8211 (m-40) cc_final: 0.7136 (m110) REVERT: F 251 LYS cc_start: 0.6909 (mptt) cc_final: 0.6600 (mmtp) REVERT: F 277 ASP cc_start: 0.8129 (t70) cc_final: 0.7880 (t0) outliers start: 38 outliers final: 32 residues processed: 180 average time/residue: 0.2175 time to fit residues: 58.4486 Evaluate side-chains 188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 1024 GLN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 194 MET Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1023 GLN Chi-restraints excluded: chain G residue 1028 SER Chi-restraints excluded: chain H residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 99 optimal weight: 40.0000 chunk 6 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133325 restraints weight = 16693.932| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.35 r_work: 0.3333 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11844 Z= 0.235 Angle : 0.616 21.889 16020 Z= 0.304 Chirality : 0.040 0.174 1766 Planarity : 0.005 0.062 2072 Dihedral : 6.605 76.114 1630 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.74 % Allowed : 13.40 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1424 helix: 1.84 (0.17), residues: 980 sheet: -1.95 (0.45), residues: 88 loop : -0.04 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 241 HIS 0.005 0.001 HIS C 43 PHE 0.030 0.002 PHE C 255 TYR 0.020 0.002 TYR C 272 ARG 0.005 0.000 ARG F 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.18 seconds wall clock time: 49 minutes 22.42 seconds (2962.42 seconds total)