Starting phenix.real_space_refine on Thu May 29 19:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixo_35800/05_2025/8ixo_35800.cif" } resolution = 4.0 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= 0.107 sd= 1.308 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 168 5.16 5 C 21108 2.51 5 N 5265 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.92s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32136 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1395, 10441 Classifications: {'peptide': 1395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 54, 'TRANS': 1340} Chain breaks: 13 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1092 Unresolved non-hydrogen angles: 1410 Unresolved non-hydrogen dihedrals: 930 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 5, 'TYR:plan': 16, 'ASN:plan1': 7, 'TRP:plan': 6, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 15, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 612 Conformer: "B" Number of residues, atoms: 1395, 10441 Classifications: {'peptide': 1395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 54, 'TRANS': 1340} Chain breaks: 13 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1092 Unresolved non-hydrogen angles: 1410 Unresolved non-hydrogen dihedrals: 930 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 5, 'TYR:plan': 16, 'ASN:plan1': 7, 'TRP:plan': 6, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 15, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 612 bond proxies already assigned to first conformer: 10663 Chain: "A" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 263 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'peptide': 2, 'undetermined': 3} Link IDs: {'TRANS': 1, None: 3} Not linked: pdbres="PLX A2601 " pdbres="PLX A2602 " Not linked: pdbres="PLX A2602 " pdbres="P5S A2603 " Not linked: pdbres="P5S A2604 " pdbres="PEE A2605 " Chain breaks: 1 Restraints were copied for chains: B, F Time building chain proxies: 38.28, per 1000 atoms: 1.19 Number of scatterers: 32136 At special positions: 0 Unit cell: (240.44, 225.07, 144.923, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 15 15.00 O 5580 8.00 N 5265 7.00 C 21108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 994 " - pdb=" SG CYS F1103 " distance=2.03 Simple disulfide: pdb=" SG CYS F1232 " - pdb=" SG CYS F1253 " distance=2.03 Simple disulfide: pdb=" SG CYS F2437 " - pdb=" SG CYS F2441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.86 Conformation dependent library (CDL) restraints added in 7.3 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8052 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 9 sheets defined 69.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'F' and resid 576 through 585 Processing helix chain 'F' and resid 586 through 596 Processing helix chain 'F' and resid 608 through 625 Processing helix chain 'F' and resid 631 through 650 Processing helix chain 'F' and resid 691 through 706 Processing helix chain 'F' and resid 708 through 715 Processing helix chain 'F' and resid 785 through 804 removed outlier: 3.600A pdb=" N SER F 789 " --> pdb=" O ASP F 785 " (cutoff:3.500A) Processing helix chain 'F' and resid 804 through 818 removed outlier: 3.931A pdb=" N HIS F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 838 Processing helix chain 'F' and resid 842 through 844 No H-bonds generated for 'chain 'F' and resid 842 through 844' Processing helix chain 'F' and resid 845 through 868 Processing helix chain 'F' and resid 924 through 950 Processing helix chain 'F' and resid 967 through 971 removed outlier: 3.975A pdb=" N ASP F 971 " --> pdb=" O GLN F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 973 through 1006 removed outlier: 6.564A pdb=" N PHE F 986 " --> pdb=" O ILE F 982 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR F 987 " --> pdb=" O ASN F 983 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS F 988 " --> pdb=" O PHE F 984 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 989 " --> pdb=" O PHE F 985 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU F 991 " --> pdb=" O TYR F 987 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU F 992 " --> pdb=" O LYS F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1007 through 1023 removed outlier: 4.212A pdb=" N ARG F1023 " --> pdb=" O ALA F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1025 through 1052 Proline residue: F1034 - end of helix Processing helix chain 'F' and resid 1073 through 1080 Processing helix chain 'F' and resid 1093 through 1113 removed outlier: 3.582A pdb=" N ASP F1097 " --> pdb=" O ASN F1093 " (cutoff:3.500A) Processing helix chain 'F' and resid 1138 through 1145 removed outlier: 4.167A pdb=" N ASN F1142 " --> pdb=" O ASN F1138 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS F1145 " --> pdb=" O PRO F1141 " (cutoff:3.500A) Processing helix chain 'F' and resid 1149 through 1159 removed outlier: 3.602A pdb=" N LEU F1153 " --> pdb=" O TYR F1149 " (cutoff:3.500A) Processing helix chain 'F' and resid 1161 through 1175 removed outlier: 3.781A pdb=" N LEU F1166 " --> pdb=" O PHE F1162 " (cutoff:3.500A) Processing helix chain 'F' and resid 1178 through 1194 Processing helix chain 'F' and resid 1194 through 1200 Processing helix chain 'F' and resid 1202 through 1233 removed outlier: 4.268A pdb=" N LEU F1229 " --> pdb=" O ASN F1225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU F1230 " --> pdb=" O MET F1226 " (cutoff:3.500A) Processing helix chain 'F' and resid 1234 through 1242 Processing helix chain 'F' and resid 1243 through 1249 removed outlier: 3.742A pdb=" N PHE F1249 " --> pdb=" O VAL F1245 " (cutoff:3.500A) Processing helix chain 'F' and resid 1280 through 1297 removed outlier: 3.612A pdb=" N SER F1284 " --> pdb=" O ILE F1280 " (cutoff:3.500A) Processing helix chain 'F' and resid 1300 through 1315 removed outlier: 4.049A pdb=" N HIS F1304 " --> pdb=" O HIS F1300 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL F1305 " --> pdb=" O TYR F1301 " (cutoff:3.500A) Processing helix chain 'F' and resid 1318 through 1363 Processing helix chain 'F' and resid 1402 through 1408 Processing helix chain 'F' and resid 1411 through 1415 Processing helix chain 'F' and resid 1506 through 1524 Processing helix chain 'F' and resid 1524 through 1544 Processing helix chain 'F' and resid 1656 through 1669 removed outlier: 3.619A pdb=" N GLN F1669 " --> pdb=" O PHE F1665 " (cutoff:3.500A) Processing helix chain 'F' and resid 1672 through 1687 Processing helix chain 'F' and resid 1688 through 1702 removed outlier: 4.070A pdb=" N TYR F1692 " --> pdb=" O GLU F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1708 through 1717 Processing helix chain 'F' and resid 1728 through 1748 Processing helix chain 'F' and resid 1771 through 1775 Processing helix chain 'F' and resid 1785 through 1803 Processing helix chain 'F' and resid 1957 through 1966 removed outlier: 3.519A pdb=" N LEU F1966 " --> pdb=" O PHE F1962 " (cutoff:3.500A) Processing helix chain 'F' and resid 1977 through 1994 Processing helix chain 'F' and resid 1995 through 1999 Processing helix chain 'F' and resid 2006 through 2013 removed outlier: 3.602A pdb=" N SER F2010 " --> pdb=" O ASP F2006 " (cutoff:3.500A) Processing helix chain 'F' and resid 2017 through 2041 Processing helix chain 'F' and resid 2043 through 2061 removed outlier: 3.616A pdb=" N VAL F2055 " --> pdb=" O VAL F2051 " (cutoff:3.500A) Processing helix chain 'F' and resid 2063 through 2069 removed outlier: 3.614A pdb=" N THR F2069 " --> pdb=" O LEU F2065 " (cutoff:3.500A) Processing helix chain 'F' and resid 2077 through 2100 removed outlier: 4.064A pdb=" N LEU F2081 " --> pdb=" O ALA F2077 " (cutoff:3.500A) Processing helix chain 'F' and resid 2115 through 2128 removed outlier: 3.537A pdb=" N VAL F2128 " --> pdb=" O GLY F2124 " (cutoff:3.500A) Processing helix chain 'F' and resid 2130 through 2143 Processing helix chain 'F' and resid 2148 through 2175 removed outlier: 3.569A pdb=" N TYR F2175 " --> pdb=" O THR F2171 " (cutoff:3.500A) Processing helix chain 'F' and resid 2184 through 2214 Proline residue: F2206 - end of helix Processing helix chain 'F' and resid 2244 through 2246 No H-bonds generated for 'chain 'F' and resid 2244 through 2246' Processing helix chain 'F' and resid 2252 through 2263 removed outlier: 3.535A pdb=" N PHE F2263 " --> pdb=" O LEU F2259 " (cutoff:3.500A) Processing helix chain 'F' and resid 2266 through 2275 Processing helix chain 'F' and resid 2276 through 2279 removed outlier: 6.291A pdb=" N GLU F2279 " --> pdb=" O TYR F2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2276 through 2279' Processing helix chain 'F' and resid 2297 through 2311 Processing helix chain 'F' and resid 2348 through 2359 Processing helix chain 'F' and resid 2422 through 2424 No H-bonds generated for 'chain 'F' and resid 2422 through 2424' Processing helix chain 'F' and resid 2458 through 2463 Processing helix chain 'F' and resid 2465 through 2473 Processing helix chain 'F' and resid 2473 through 2484 Processing helix chain 'F' and resid 2489 through 2493 removed outlier: 4.399A pdb=" N MET F2493 " --> pdb=" O HIS F2490 " (cutoff:3.500A) Processing helix chain 'F' and resid 2500 through 2517 removed outlier: 3.592A pdb=" N GLU F2515 " --> pdb=" O PHE F2511 " (cutoff:3.500A) Processing helix chain 'F' and resid 2518 through 2535 Processing helix chain 'F' and resid 2535 through 2543 Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 631 through 650 Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 785 through 804 removed outlier: 3.600A pdb=" N SER A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 818 removed outlier: 3.931A pdb=" N HIS A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 838 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 868 Processing helix chain 'A' and resid 924 through 950 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.975A pdb=" N ASP A 971 " --> pdb=" O GLN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1006 removed outlier: 6.564A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 988 " --> pdb=" O PHE A 984 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 4.212A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1052 Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1073 through 1080 Processing helix chain 'A' and resid 1093 through 1113 removed outlier: 3.582A pdb=" N ASP A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1145 removed outlier: 4.167A pdb=" N ASN A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A1145 " --> pdb=" O PRO A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.603A pdb=" N LEU A1153 " --> pdb=" O TYR A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1175 removed outlier: 3.781A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1202 through 1233 removed outlier: 4.268A pdb=" N LEU A1229 " --> pdb=" O ASN A1225 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A1230 " --> pdb=" O MET A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1242 Processing helix chain 'A' and resid 1243 through 1249 removed outlier: 3.742A pdb=" N PHE A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1297 removed outlier: 3.612A pdb=" N SER A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1315 removed outlier: 4.049A pdb=" N HIS A1304 " --> pdb=" O HIS A1300 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A1305 " --> pdb=" O TYR A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1363 Processing helix chain 'A' and resid 1402 through 1408 Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1506 through 1524 Processing helix chain 'A' and resid 1524 through 1544 Processing helix chain 'A' and resid 1656 through 1669 removed outlier: 3.620A pdb=" N GLN A1669 " --> pdb=" O PHE A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1687 Processing helix chain 'A' and resid 1688 through 1702 removed outlier: 4.070A pdb=" N TYR A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1717 Processing helix chain 'A' and resid 1728 through 1748 Processing helix chain 'A' and resid 1771 through 1775 Processing helix chain 'A' and resid 1785 through 1803 Processing helix chain 'A' and resid 1957 through 1966 removed outlier: 3.519A pdb=" N LEU A1966 " --> pdb=" O PHE A1962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1994 Processing helix chain 'A' and resid 1995 through 1999 Processing helix chain 'A' and resid 2006 through 2013 removed outlier: 3.602A pdb=" N SER A2010 " --> pdb=" O ASP A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2041 Processing helix chain 'A' and resid 2043 through 2061 removed outlier: 3.617A pdb=" N VAL A2055 " --> pdb=" O VAL A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2063 through 2069 removed outlier: 3.614A pdb=" N THR A2069 " --> pdb=" O LEU A2065 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2100 removed outlier: 4.063A pdb=" N LEU A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 3.537A pdb=" N VAL A2128 " --> pdb=" O GLY A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2143 Processing helix chain 'A' and resid 2148 through 2175 removed outlier: 3.570A pdb=" N TYR A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2214 Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2244 through 2246 No H-bonds generated for 'chain 'A' and resid 2244 through 2246' Processing helix chain 'A' and resid 2252 through 2263 removed outlier: 3.536A pdb=" N PHE A2263 " --> pdb=" O LEU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2275 Processing helix chain 'A' and resid 2276 through 2279 removed outlier: 6.291A pdb=" N GLU A2279 " --> pdb=" O TYR A2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2276 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2348 through 2359 Processing helix chain 'A' and resid 2422 through 2424 No H-bonds generated for 'chain 'A' and resid 2422 through 2424' Processing helix chain 'A' and resid 2458 through 2463 Processing helix chain 'A' and resid 2465 through 2473 Processing helix chain 'A' and resid 2473 through 2484 Processing helix chain 'A' and resid 2489 through 2493 removed outlier: 4.398A pdb=" N MET A2493 " --> pdb=" O HIS A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2517 removed outlier: 3.591A pdb=" N GLU A2515 " --> pdb=" O PHE A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2535 Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'B' and resid 577 through 585 Processing helix chain 'B' and resid 586 through 596 Processing helix chain 'B' and resid 608 through 625 Processing helix chain 'B' and resid 631 through 650 Processing helix chain 'B' and resid 691 through 706 Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'B' and resid 785 through 804 removed outlier: 3.601A pdb=" N SER B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 818 removed outlier: 3.931A pdb=" N HIS B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 838 Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 845 through 868 Processing helix chain 'B' and resid 924 through 950 Processing helix chain 'B' and resid 967 through 971 removed outlier: 3.974A pdb=" N ASP B 971 " --> pdb=" O GLN B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1006 removed outlier: 6.563A pdb=" N PHE B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 988 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 989 " --> pdb=" O PHE B 985 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1023 removed outlier: 4.212A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1052 Proline residue: B1034 - end of helix Processing helix chain 'B' and resid 1073 through 1080 Processing helix chain 'B' and resid 1093 through 1113 removed outlier: 3.582A pdb=" N ASP B1097 " --> pdb=" O ASN B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1145 removed outlier: 4.168A pdb=" N ASN B1142 " --> pdb=" O ASN B1138 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B1145 " --> pdb=" O PRO B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1159 removed outlier: 3.602A pdb=" N LEU B1153 " --> pdb=" O TYR B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1175 removed outlier: 3.781A pdb=" N LEU B1166 " --> pdb=" O PHE B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1194 Processing helix chain 'B' and resid 1194 through 1200 Processing helix chain 'B' and resid 1202 through 1233 removed outlier: 4.269A pdb=" N LEU B1229 " --> pdb=" O ASN B1225 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B1230 " --> pdb=" O MET B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1234 through 1242 Processing helix chain 'B' and resid 1243 through 1249 removed outlier: 3.741A pdb=" N PHE B1249 " --> pdb=" O VAL B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1297 removed outlier: 3.613A pdb=" N SER B1284 " --> pdb=" O ILE B1280 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1315 removed outlier: 3.998A pdb=" N HIS B1304 " --> pdb=" O HIS B1300 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B1305 " --> pdb=" O TYR B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1318 through 1363 Processing helix chain 'B' and resid 1402 through 1408 Processing helix chain 'B' and resid 1411 through 1415 Processing helix chain 'B' and resid 1506 through 1524 Processing helix chain 'B' and resid 1524 through 1544 Processing helix chain 'B' and resid 1656 through 1669 removed outlier: 3.620A pdb=" N GLN B1669 " --> pdb=" O PHE B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1687 Processing helix chain 'B' and resid 1688 through 1702 removed outlier: 4.071A pdb=" N TYR B1692 " --> pdb=" O GLU B1688 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1717 Processing helix chain 'B' and resid 1728 through 1748 Processing helix chain 'B' and resid 1771 through 1775 Processing helix chain 'B' and resid 1785 through 1803 Processing helix chain 'B' and resid 1957 through 1966 removed outlier: 3.519A pdb=" N LEU B1966 " --> pdb=" O PHE B1962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1977 through 1994 Processing helix chain 'B' and resid 1995 through 1999 Processing helix chain 'B' and resid 2006 through 2013 removed outlier: 3.601A pdb=" N SER B2010 " --> pdb=" O ASP B2006 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2041 Processing helix chain 'B' and resid 2043 through 2061 removed outlier: 3.616A pdb=" N VAL B2055 " --> pdb=" O VAL B2051 " (cutoff:3.500A) Processing helix chain 'B' and resid 2063 through 2069 removed outlier: 3.614A pdb=" N THR B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2100 removed outlier: 4.062A pdb=" N LEU B2081 " --> pdb=" O ALA B2077 " (cutoff:3.500A) Processing helix chain 'B' and resid 2115 through 2128 removed outlier: 3.537A pdb=" N VAL B2128 " --> pdb=" O GLY B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2143 Processing helix chain 'B' and resid 2148 through 2175 removed outlier: 3.571A pdb=" N TYR B2175 " --> pdb=" O THR B2171 " (cutoff:3.500A) Processing helix chain 'B' and resid 2184 through 2214 Proline residue: B2206 - end of helix Processing helix chain 'B' and resid 2244 through 2246 No H-bonds generated for 'chain 'B' and resid 2244 through 2246' Processing helix chain 'B' and resid 2252 through 2263 removed outlier: 3.536A pdb=" N PHE B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2266 through 2275 Processing helix chain 'B' and resid 2276 through 2279 removed outlier: 6.291A pdb=" N GLU B2279 " --> pdb=" O TYR B2276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2276 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2348 through 2359 Processing helix chain 'B' and resid 2422 through 2424 No H-bonds generated for 'chain 'B' and resid 2422 through 2424' Processing helix chain 'B' and resid 2458 through 2463 Processing helix chain 'B' and resid 2465 through 2473 Processing helix chain 'B' and resid 2473 through 2484 Processing helix chain 'B' and resid 2489 through 2493 removed outlier: 4.399A pdb=" N MET B2493 " --> pdb=" O HIS B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2500 through 2517 removed outlier: 3.592A pdb=" N GLU B2515 " --> pdb=" O PHE B2511 " (cutoff:3.500A) Processing helix chain 'B' and resid 2518 through 2535 Processing helix chain 'B' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'F' and resid 2237 through 2241 removed outlier: 7.014A pdb=" N LEU F2232 " --> pdb=" O PRO F2237 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP F2225 " --> pdb=" O GLN F2324 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR F2336 " --> pdb=" O PHE F2323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 2248 through 2250 removed outlier: 3.510A pdb=" N ASN F2385 " --> pdb=" O ARG F2377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 2366 through 2372 removed outlier: 3.589A pdb=" N VAL F2366 " --> pdb=" O ILE F2403 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS F2370 " --> pdb=" O LEU F2399 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F2399 " --> pdb=" O HIS F2370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2237 through 2241 removed outlier: 7.014A pdb=" N LEU A2232 " --> pdb=" O PRO A2237 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A2225 " --> pdb=" O GLN A2324 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A2336 " --> pdb=" O PHE A2323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 3.510A pdb=" N ASN A2385 " --> pdb=" O ARG A2377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 3.589A pdb=" N VAL A2366 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A2370 " --> pdb=" O LEU A2399 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A2399 " --> pdb=" O HIS A2370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2237 through 2241 removed outlier: 7.015A pdb=" N LEU B2232 " --> pdb=" O PRO B2237 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B2225 " --> pdb=" O GLN B2324 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B2336 " --> pdb=" O PHE B2323 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 3.510A pdb=" N ASN B2385 " --> pdb=" O ARG B2377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 3.590A pdb=" N VAL B2366 " --> pdb=" O ILE B2403 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B2370 " --> pdb=" O LEU B2399 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B2399 " --> pdb=" O HIS B2370 " (cutoff:3.500A) 2140 hydrogen bonds defined for protein. 6363 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: 12.37 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5492 1.33 - 1.45: 8452 1.45 - 1.58: 18582 1.58 - 1.70: 33 1.70 - 1.82: 258 Bond restraints: 32817 Sorted by residual: bond pdb=" C18 PEE F2605 " pdb=" C19 PEE F2605 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 PEE B2605 " pdb=" C19 PEE B2605 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 PEE A2605 " pdb=" C19 PEE A2605 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C38 PEE F2605 " pdb=" C39 PEE F2605 " ideal model delta sigma weight residual 1.523 1.310 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C38 PEE A2605 " pdb=" C39 PEE A2605 " ideal model delta sigma weight residual 1.523 1.310 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 32812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 44007 2.97 - 5.93: 444 5.93 - 8.90: 69 8.90 - 11.87: 12 11.87 - 14.84: 12 Bond angle restraints: 44544 Sorted by residual: angle pdb=" C38 PEE A2605 " pdb=" C39 PEE A2605 " pdb=" C40 PEE A2605 " ideal model delta sigma weight residual 112.47 127.31 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C38 PEE B2605 " pdb=" C39 PEE B2605 " pdb=" C40 PEE B2605 " ideal model delta sigma weight residual 112.47 127.30 -14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C38 PEE F2605 " pdb=" C39 PEE F2605 " pdb=" C40 PEE F2605 " ideal model delta sigma weight residual 112.47 127.29 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" O3P PEE F2605 " pdb=" P PEE F2605 " pdb=" O4P PEE F2605 " ideal model delta sigma weight residual 92.91 106.26 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O3P PEE B2605 " pdb=" P PEE B2605 " pdb=" O4P PEE B2605 " ideal model delta sigma weight residual 92.91 106.25 -13.34 3.00e+00 1.11e-01 1.98e+01 ... (remaining 44539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.99: 18768 29.99 - 59.99: 721 59.99 - 89.98: 92 89.98 - 119.98: 45 119.98 - 149.97: 42 Dihedral angle restraints: 19668 sinusoidal: 7329 harmonic: 12339 Sorted by residual: dihedral pdb=" CB CYS F1232 " pdb=" SG CYS F1232 " pdb=" SG CYS F1253 " pdb=" CB CYS F1253 " ideal model delta sinusoidal sigma weight residual -86.00 -153.59 67.59 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CA ARG B1147 " pdb=" C ARG B1147 " pdb=" N SER B1148 " pdb=" CA SER B1148 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG F1147 " pdb=" C ARG F1147 " pdb=" N SER F1148 " pdb=" CA SER F1148 " ideal model delta harmonic sigma weight residual 180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 19665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4833 0.077 - 0.155: 319 0.155 - 0.232: 8 0.232 - 0.310: 3 0.310 - 0.387: 3 Chirality restraints: 5166 Sorted by residual: chirality pdb=" C6 PLX F2601 " pdb=" C7 PLX F2601 " pdb=" O6 PLX F2601 " pdb=" O7 PLX F2601 " both_signs ideal model delta sigma weight residual False 2.01 2.40 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C6 PLX B2601 " pdb=" C7 PLX B2601 " pdb=" O6 PLX B2601 " pdb=" O7 PLX B2601 " both_signs ideal model delta sigma weight residual False 2.01 2.40 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C6 PLX A2601 " pdb=" C7 PLX A2601 " pdb=" O6 PLX A2601 " pdb=" O7 PLX A2601 " both_signs ideal model delta sigma weight residual False 2.01 2.39 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 5163 not shown) Planarity restraints: 5511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B2319 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C PHE B2319 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE B2319 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B2320 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A2319 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C PHE A2319 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE A2319 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A2320 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F2319 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C PHE F2319 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE F2319 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F2320 " 0.012 2.00e-02 2.50e+03 ... (remaining 5508 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 213 2.60 - 3.18: 28128 3.18 - 3.75: 49944 3.75 - 4.33: 60954 4.33 - 4.90: 102156 Nonbonded interactions: 241395 Sorted by model distance: nonbonded pdb=" SG CYS B2437 " pdb=" SG CYS B2441 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A2437 " pdb=" SG CYS A2441 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B1232 " pdb=" SG CYS B1253 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A1232 " pdb=" SG CYS A1253 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 994 " pdb=" SG CYS A1103 " model vdw 2.033 3.760 ... (remaining 241390 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.130 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: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 93.280 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.005 0.216 32820 Z= 0.253 Angle : 0.755 14.837 44550 Z= 0.358 Chirality : 0.042 0.387 5166 Planarity : 0.004 0.048 5511 Dihedral : 18.882 149.971 11607 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.10 % Allowed : 7.38 % Favored : 92.51 % 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: 0.57 (0.14), residues: 4104 helix: 1.67 (0.10), residues: 2748 sheet: -1.01 (0.32), residues: 282 loop : -2.78 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 836 HIS 0.006 0.001 HIS A1403 PHE 0.022 0.001 PHE A2062 TYR 0.011 0.001 TYR F2470 ARG 0.011 0.000 ARG A1724 Details of bonding type rmsd hydrogen bonds : bond 0.11959 ( 2140) hydrogen bonds : angle 5.26395 ( 6363) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.86677 ( 6) covalent geometry : bond 0.00512 (32817) covalent geometry : angle 0.75524 (44544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 3.428 Fit side-chains REVERT: F 1152 MET cc_start: 0.8558 (mtt) cc_final: 0.8345 (mtt) REVERT: F 2241 MET cc_start: 0.8421 (tpp) cc_final: 0.8127 (tpt) REVERT: B 1072 MET cc_start: 0.7290 (ptp) cc_final: 0.7072 (ptt) REVERT: B 1215 LEU cc_start: 0.8791 (tt) cc_final: 0.8285 (mt) REVERT: B 1349 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7584 (tpp) REVERT: B 2509 ASP cc_start: 0.8200 (m-30) cc_final: 0.7855 (m-30) outliers start: 3 outliers final: 2 residues processed: 223 average time/residue: 0.3515 time to fit residues: 139.5680 Evaluate side-chains 221 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1349 MET Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 1349 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 0.6980 chunk 316 optimal weight: 6.9990 chunk 175 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 213 optimal weight: 0.2980 chunk 168 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1304 HIS F2118 ASN A1304 HIS A2118 ASN A2151 ASN B1304 HIS B2118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067201 restraints weight = 140591.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069128 restraints weight = 67149.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070397 restraints weight = 41566.237| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32820 Z= 0.132 Angle : 0.581 7.173 44550 Z= 0.297 Chirality : 0.039 0.153 5166 Planarity : 0.004 0.045 5511 Dihedral : 17.716 159.777 5286 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.96 % Allowed : 8.21 % Favored : 90.84 % 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: 0.94 (0.14), residues: 4104 helix: 1.89 (0.10), residues: 2790 sheet: -0.83 (0.32), residues: 282 loop : -2.63 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B2142 HIS 0.006 0.001 HIS A1403 PHE 0.021 0.001 PHE A2062 TYR 0.015 0.001 TYR B2470 ARG 0.003 0.000 ARG B1295 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 2140) hydrogen bonds : angle 4.24572 ( 6363) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.66177 ( 6) covalent geometry : bond 0.00287 (32817) covalent geometry : angle 0.58056 (44544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 3.435 Fit side-chains REVERT: F 1226 MET cc_start: 0.8468 (tpp) cc_final: 0.8191 (mmm) REVERT: F 2053 LEU cc_start: 0.8940 (tp) cc_final: 0.8684 (tp) REVERT: F 2241 MET cc_start: 0.8328 (tpp) cc_final: 0.8122 (tpt) REVERT: A 2031 MET cc_start: 0.8302 (mtm) cc_final: 0.8081 (mtp) REVERT: B 1072 MET cc_start: 0.7290 (ptp) cc_final: 0.7060 (ptt) REVERT: B 1731 MET cc_start: 0.9024 (tpp) cc_final: 0.8799 (mmp) REVERT: B 2509 ASP cc_start: 0.8179 (m-30) cc_final: 0.7848 (m-30) outliers start: 28 outliers final: 17 residues processed: 236 average time/residue: 0.3525 time to fit residues: 148.5254 Evaluate side-chains 225 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 2304 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 367 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 323 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 254 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 83 optimal weight: 0.0040 chunk 411 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2151 ASN B2151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067995 restraints weight = 164018.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070300 restraints weight = 73855.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071562 restraints weight = 40012.556| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32820 Z= 0.110 Angle : 0.538 12.173 44550 Z= 0.272 Chirality : 0.038 0.147 5166 Planarity : 0.004 0.037 5511 Dihedral : 16.360 172.039 5277 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.13 % Allowed : 10.12 % Favored : 88.75 % 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: 1.12 (0.14), residues: 4104 helix: 2.00 (0.10), residues: 2814 sheet: -0.75 (0.32), residues: 276 loop : -2.57 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 836 HIS 0.008 0.001 HIS F1304 PHE 0.019 0.001 PHE A2062 TYR 0.023 0.001 TYR B1046 ARG 0.002 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 2140) hydrogen bonds : angle 3.99277 ( 6363) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.63589 ( 6) covalent geometry : bond 0.00236 (32817) covalent geometry : angle 0.53811 (44544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1226 MET cc_start: 0.8535 (tpp) cc_final: 0.8285 (mmm) REVERT: F 2053 LEU cc_start: 0.8879 (tp) cc_final: 0.8655 (tp) REVERT: A 2263 PHE cc_start: 0.8248 (m-80) cc_final: 0.7870 (m-80) REVERT: B 2270 MET cc_start: 0.8132 (mmm) cc_final: 0.7918 (mmm) REVERT: B 2309 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7839 (m-10) REVERT: B 2408 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 2509 ASP cc_start: 0.8267 (m-30) cc_final: 0.7850 (m-30) outliers start: 33 outliers final: 25 residues processed: 243 average time/residue: 0.3570 time to fit residues: 153.1901 Evaluate side-chains 233 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1245 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 2309 TYR Chi-restraints excluded: chain B residue 2521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 252 optimal weight: 2.9990 chunk 341 optimal weight: 8.9990 chunk 133 optimal weight: 0.0050 chunk 104 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 288 optimal weight: 30.0000 chunk 301 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1047 GLN F1225 ASN F2356 GLN A1047 GLN ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 ASN A1304 HIS A2356 GLN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1225 ASN ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2356 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065346 restraints weight = 153366.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067544 restraints weight = 71448.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068748 restraints weight = 39696.258| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32820 Z= 0.159 Angle : 0.573 9.421 44550 Z= 0.293 Chirality : 0.039 0.158 5166 Planarity : 0.004 0.036 5511 Dihedral : 15.491 161.394 5277 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.95 % Allowed : 10.80 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.17 (0.14), residues: 4104 helix: 2.04 (0.10), residues: 2817 sheet: -0.66 (0.32), residues: 276 loop : -2.61 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 836 HIS 0.005 0.001 HIS A1304 PHE 0.027 0.001 PHE B1143 TYR 0.016 0.001 TYR A1046 ARG 0.003 0.000 ARG F1724 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 2140) hydrogen bonds : angle 4.01751 ( 6363) SS BOND : bond 0.00302 ( 3) SS BOND : angle 0.67655 ( 6) covalent geometry : bond 0.00368 (32817) covalent geometry : angle 0.57319 (44544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 203 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2053 LEU cc_start: 0.8955 (tp) cc_final: 0.8723 (tp) REVERT: A 2263 PHE cc_start: 0.8267 (m-80) cc_final: 0.7927 (m-80) REVERT: B 1238 MET cc_start: 0.6994 (tpp) cc_final: 0.6711 (tpt) REVERT: B 2270 MET cc_start: 0.8078 (mmm) cc_final: 0.7855 (mmm) REVERT: B 2509 ASP cc_start: 0.8145 (m-30) cc_final: 0.7938 (m-30) outliers start: 57 outliers final: 36 residues processed: 239 average time/residue: 0.3603 time to fit residues: 151.2871 Evaluate side-chains 236 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1011 ILE Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1739 VAL Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2064 ILE Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2521 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1245 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1726 SER Chi-restraints excluded: chain B residue 2002 SER Chi-restraints excluded: chain B residue 2304 MET Chi-restraints excluded: chain B residue 2521 LEU Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 199 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 330 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 387 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2435 GLN ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2435 GLN B1047 GLN ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065369 restraints weight = 161256.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067732 restraints weight = 74459.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.068318 restraints weight = 39493.538| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32820 Z= 0.145 Angle : 0.546 7.650 44550 Z= 0.281 Chirality : 0.039 0.155 5166 Planarity : 0.004 0.037 5511 Dihedral : 15.078 160.390 5277 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.98 % Allowed : 11.97 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.22 (0.14), residues: 4104 helix: 2.07 (0.10), residues: 2817 sheet: -0.60 (0.32), residues: 276 loop : -2.59 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 836 HIS 0.007 0.001 HIS A1304 PHE 0.020 0.001 PHE A1143 TYR 0.024 0.001 TYR B1046 ARG 0.004 0.000 ARG B2407 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 2140) hydrogen bonds : angle 3.97236 ( 6363) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.64890 ( 6) covalent geometry : bond 0.00331 (32817) covalent geometry : angle 0.54612 (44544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 2121 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8724 (tp) REVERT: A 2263 PHE cc_start: 0.8468 (m-80) cc_final: 0.8125 (m-80) REVERT: B 2121 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 2270 MET cc_start: 0.8215 (mmm) cc_final: 0.7987 (mmm) REVERT: B 2509 ASP cc_start: 0.8267 (m-30) cc_final: 0.8004 (m-30) outliers start: 58 outliers final: 40 residues processed: 236 average time/residue: 0.3432 time to fit residues: 143.2901 Evaluate side-chains 244 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1011 ILE Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1220 VAL Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1716 LEU Chi-restraints excluded: chain F residue 1739 VAL Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2061 MET Chi-restraints excluded: chain A residue 2064 ILE Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2521 LEU Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1222 ILE Chi-restraints excluded: chain B residue 1245 VAL Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1726 SER Chi-restraints excluded: chain B residue 2002 SER Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2121 LEU Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 122 optimal weight: 1.9990 chunk 386 optimal weight: 7.9990 chunk 249 optimal weight: 0.0370 chunk 171 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 139 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 96 optimal weight: 0.0370 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067420 restraints weight = 137186.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069637 restraints weight = 68106.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070581 restraints weight = 36645.771| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32820 Z= 0.102 Angle : 0.508 11.934 44550 Z= 0.259 Chirality : 0.038 0.142 5166 Planarity : 0.003 0.038 5511 Dihedral : 14.450 150.408 5277 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.54 % Allowed : 12.68 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.41 (0.14), residues: 4104 helix: 2.20 (0.10), residues: 2817 sheet: -0.43 (0.32), residues: 276 loop : -2.48 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 836 HIS 0.004 0.001 HIS B1403 PHE 0.019 0.001 PHE A1143 TYR 0.022 0.001 TYR B1046 ARG 0.002 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 2140) hydrogen bonds : angle 3.81396 ( 6363) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.60692 ( 6) covalent geometry : bond 0.00218 (32817) covalent geometry : angle 0.50822 (44544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8675 (tp) REVERT: F 2263 PHE cc_start: 0.8551 (m-80) cc_final: 0.8304 (m-80) REVERT: F 2509 ASP cc_start: 0.8304 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1700 MET cc_start: 0.8658 (mtp) cc_final: 0.8294 (mtp) REVERT: A 2121 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 2263 PHE cc_start: 0.8233 (m-80) cc_final: 0.7907 (m-80) REVERT: A 2309 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 1238 MET cc_start: 0.7427 (tpt) cc_final: 0.7200 (tpt) REVERT: B 2121 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8680 (tp) REVERT: B 2309 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: B 2408 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 2472 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 2509 ASP cc_start: 0.8219 (m-30) cc_final: 0.7941 (m-30) outliers start: 45 outliers final: 26 residues processed: 247 average time/residue: 0.3449 time to fit residues: 150.7881 Evaluate side-chains 235 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2309 TYR Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1245 VAL Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 2121 LEU Chi-restraints excluded: chain B residue 2309 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 259 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 389 optimal weight: 0.0670 chunk 379 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 402 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066832 restraints weight = 211249.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068961 restraints weight = 92308.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069896 restraints weight = 48840.018| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32820 Z= 0.103 Angle : 0.507 12.044 44550 Z= 0.257 Chirality : 0.038 0.142 5166 Planarity : 0.003 0.038 5511 Dihedral : 14.201 145.555 5277 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.61 % Allowed : 13.20 % Favored : 85.20 % 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: 1.48 (0.14), residues: 4104 helix: 2.22 (0.10), residues: 2826 sheet: -0.33 (0.32), residues: 276 loop : -2.40 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 836 HIS 0.005 0.001 HIS A1304 PHE 0.016 0.001 PHE A1143 TYR 0.011 0.001 TYR B2470 ARG 0.002 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 2140) hydrogen bonds : angle 3.74580 ( 6363) SS BOND : bond 0.00214 ( 3) SS BOND : angle 0.57727 ( 6) covalent geometry : bond 0.00225 (32817) covalent geometry : angle 0.50686 (44544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8700 (tp) REVERT: F 2263 PHE cc_start: 0.8506 (m-80) cc_final: 0.8282 (m-80) REVERT: A 1700 MET cc_start: 0.8642 (mtp) cc_final: 0.8190 (mtp) REVERT: A 2121 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 2309 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B 2121 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8711 (tp) REVERT: B 2270 MET cc_start: 0.8553 (mmm) cc_final: 0.7877 (mmm) REVERT: B 2309 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7732 (t80) REVERT: B 2408 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 2509 ASP cc_start: 0.8079 (m-30) cc_final: 0.7830 (m-30) outliers start: 47 outliers final: 36 residues processed: 245 average time/residue: 0.3514 time to fit residues: 153.4472 Evaluate side-chains 242 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1222 ILE Chi-restraints excluded: chain F residue 1505 LEU Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2309 TYR Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 836 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1348 GLN Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 2121 LEU Chi-restraints excluded: chain B residue 2309 TYR Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 376 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 365 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 chunk 347 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1669 GLN ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1669 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065357 restraints weight = 173743.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067490 restraints weight = 75718.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068045 restraints weight = 42975.409| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32820 Z= 0.145 Angle : 0.536 12.332 44550 Z= 0.273 Chirality : 0.039 0.145 5166 Planarity : 0.003 0.036 5511 Dihedral : 14.207 141.091 5277 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.98 % Allowed : 13.16 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.46 (0.14), residues: 4104 helix: 2.20 (0.10), residues: 2826 sheet: -0.34 (0.32), residues: 276 loop : -2.43 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 836 HIS 0.006 0.001 HIS A1304 PHE 0.019 0.001 PHE A1143 TYR 0.027 0.001 TYR B1046 ARG 0.002 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 2140) hydrogen bonds : angle 3.81651 ( 6363) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.61706 ( 6) covalent geometry : bond 0.00336 (32817) covalent geometry : angle 0.53647 (44544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8698 (tp) REVERT: F 2509 ASP cc_start: 0.8179 (m-30) cc_final: 0.7863 (m-30) REVERT: A 1700 MET cc_start: 0.8716 (mtp) cc_final: 0.8299 (mtp) REVERT: A 2121 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 2309 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B 1238 MET cc_start: 0.7321 (tpt) cc_final: 0.7056 (tpt) REVERT: B 2121 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 2270 MET cc_start: 0.8575 (mmm) cc_final: 0.7973 (mmm) REVERT: B 2309 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (m-10) REVERT: B 2408 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 2509 ASP cc_start: 0.8066 (m-30) cc_final: 0.7817 (m-30) outliers start: 58 outliers final: 36 residues processed: 244 average time/residue: 0.3650 time to fit residues: 154.8138 Evaluate side-chains 238 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1011 ILE Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1222 ILE Chi-restraints excluded: chain F residue 1505 LEU Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 836 TRP Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2309 TYR Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 836 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1348 GLN Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1726 SER Chi-restraints excluded: chain B residue 2121 LEU Chi-restraints excluded: chain B residue 2309 TYR Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 88 optimal weight: 3.9990 chunk 362 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 361 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066167 restraints weight = 192069.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068149 restraints weight = 87238.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068933 restraints weight = 48302.854| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32820 Z= 0.110 Angle : 0.512 9.160 44550 Z= 0.261 Chirality : 0.038 0.144 5166 Planarity : 0.003 0.039 5511 Dihedral : 14.029 139.521 5277 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.71 % Allowed : 13.40 % Favored : 84.89 % 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: 1.52 (0.14), residues: 4104 helix: 2.26 (0.10), residues: 2820 sheet: -0.36 (0.32), residues: 276 loop : -2.40 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 836 HIS 0.006 0.001 HIS F1699 PHE 0.022 0.001 PHE F2062 TYR 0.022 0.001 TYR B1046 ARG 0.002 0.000 ARG F1724 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 2140) hydrogen bonds : angle 3.75263 ( 6363) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.57732 ( 6) covalent geometry : bond 0.00245 (32817) covalent geometry : angle 0.51154 (44544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8678 (tp) REVERT: F 2509 ASP cc_start: 0.8176 (m-30) cc_final: 0.7852 (m-30) REVERT: A 1700 MET cc_start: 0.8677 (mtp) cc_final: 0.8260 (mtp) REVERT: A 2121 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8726 (tp) REVERT: B 2270 MET cc_start: 0.8558 (mmm) cc_final: 0.7941 (mmm) REVERT: B 2309 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: B 2408 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 2509 ASP cc_start: 0.8057 (m-30) cc_final: 0.7806 (m-30) outliers start: 50 outliers final: 38 residues processed: 241 average time/residue: 0.3486 time to fit residues: 148.1454 Evaluate side-chains 240 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1220 VAL Chi-restraints excluded: chain F residue 1222 ILE Chi-restraints excluded: chain F residue 1505 LEU Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 836 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1348 GLN Chi-restraints excluded: chain B residue 1349 MET Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1726 SER Chi-restraints excluded: chain B residue 2309 TYR Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 171 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 36 optimal weight: 0.0020 chunk 265 optimal weight: 0.9980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065585 restraints weight = 193976.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067237 restraints weight = 88569.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067976 restraints weight = 51041.441| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32820 Z= 0.128 Angle : 0.525 8.775 44550 Z= 0.268 Chirality : 0.038 0.143 5166 Planarity : 0.003 0.039 5511 Dihedral : 13.959 140.097 5277 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.50 % Allowed : 13.57 % Favored : 84.92 % 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: 1.51 (0.14), residues: 4104 helix: 2.24 (0.10), residues: 2823 sheet: -0.35 (0.32), residues: 276 loop : -2.40 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 836 HIS 0.006 0.001 HIS A1304 PHE 0.024 0.001 PHE F2263 TYR 0.024 0.001 TYR B1046 ARG 0.002 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 2140) hydrogen bonds : angle 3.78448 ( 6363) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.59933 ( 6) covalent geometry : bond 0.00293 (32817) covalent geometry : angle 0.52521 (44544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2121 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8699 (tp) REVERT: F 2509 ASP cc_start: 0.8165 (m-30) cc_final: 0.7845 (m-30) REVERT: A 1700 MET cc_start: 0.8706 (mtp) cc_final: 0.8290 (mtp) REVERT: A 2121 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8729 (tp) REVERT: B 2270 MET cc_start: 0.8576 (mmm) cc_final: 0.7951 (mmm) REVERT: B 2309 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: B 2408 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 2509 ASP cc_start: 0.8070 (m-30) cc_final: 0.7825 (m-30) outliers start: 44 outliers final: 40 residues processed: 228 average time/residue: 0.3561 time to fit residues: 143.2173 Evaluate side-chains 244 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS Chi-restraints excluded: chain F residue 1143 PHE Chi-restraints excluded: chain F residue 1220 VAL Chi-restraints excluded: chain F residue 1222 ILE Chi-restraints excluded: chain F residue 1505 LEU Chi-restraints excluded: chain F residue 1540 LEU Chi-restraints excluded: chain F residue 1663 GLU Chi-restraints excluded: chain F residue 1689 LEU Chi-restraints excluded: chain F residue 1690 LEU Chi-restraints excluded: chain F residue 1791 MET Chi-restraints excluded: chain F residue 2121 LEU Chi-restraints excluded: chain F residue 2493 MET Chi-restraints excluded: chain F residue 2542 TRP Chi-restraints excluded: chain A residue 836 TRP Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1663 GLU Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2197 LEU Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2258 GLU Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2542 TRP Chi-restraints excluded: chain B residue 836 TRP Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1013 HIS Chi-restraints excluded: chain B residue 1143 PHE Chi-restraints excluded: chain B residue 1348 GLN Chi-restraints excluded: chain B residue 1349 MET Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1663 GLU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1726 SER Chi-restraints excluded: chain B residue 2309 TYR Chi-restraints excluded: chain B residue 2542 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 299 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 212 optimal weight: 0.0570 chunk 133 optimal weight: 0.0670 chunk 337 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 377 optimal weight: 0.8980 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065667 restraints weight = 181756.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068261 restraints weight = 82229.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068806 restraints weight = 41979.640| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32820 Z= 0.120 Angle : 0.521 9.894 44550 Z= 0.265 Chirality : 0.038 0.145 5166 Planarity : 0.003 0.039 5511 Dihedral : 13.834 142.424 5277 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.57 % Allowed : 13.64 % Favored : 84.79 % 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: 1.53 (0.14), residues: 4104 helix: 2.26 (0.10), residues: 2823 sheet: -0.35 (0.32), residues: 276 loop : -2.39 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 836 HIS 0.005 0.001 HIS A1304 PHE 0.019 0.001 PHE F2062 TYR 0.023 0.001 TYR B1046 ARG 0.002 0.000 ARG B2402 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 2140) hydrogen bonds : angle 3.76952 ( 6363) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.59674 ( 6) covalent geometry : bond 0.00275 (32817) covalent geometry : angle 0.52120 (44544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9404.10 seconds wall clock time: 165 minutes 31.01 seconds (9931.01 seconds total)