Starting phenix.real_space_refine on Tue Aug 26 02:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixo_35800/08_2025/8ixo_35800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixo_35800/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ixo_35800/08_2025/8ixo_35800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixo_35800/08_2025/8ixo_35800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ixo_35800/08_2025/8ixo_35800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixo_35800/08_2025/8ixo_35800.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32136 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" 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: {'GLU:plan': 15, 'TYR:plan': 16, 'TRP:plan': 6, 'PHE:plan': 18, 'ARG:plan': 28, 'GLN:plan1': 13, 'HIS:plan': 10, 'ASP:plan': 5, 'ASN:plan1': 7} 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: {'GLU:plan': 15, 'TYR:plan': 16, 'TRP:plan': 6, 'PHE:plan': 18, 'ARG:plan': 28, 'GLN:plan1': 13, 'HIS:plan': 10, 'ASP:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 612 bond proxies already assigned to first conformer: 10663 Chain: "F" 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 F2601 " pdbres="PLX F2602 " Not linked: pdbres="PLX F2602 " pdbres="P5S F2603 " Not linked: pdbres="P5S F2604 " pdbres="PEE F2605 " Chain breaks: 1 Restraints were copied for chains: A, B Time building chain proxies: 16.65, per 1000 atoms: 0.52 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=9, 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 Simple disulfide: pdb=" SG CYS A 994 " - pdb=" SG CYS A1103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 994 " - pdb=" SG CYS B1103 " distance=2.03 Simple disulfide: pdb=" SG CYS A1232 " - pdb=" SG CYS A1253 " distance=2.03 Simple disulfide: pdb=" SG CYS B1232 " - pdb=" SG CYS B1253 " distance=2.03 Simple disulfide: pdb=" SG CYS A2437 " - pdb=" SG CYS A2441 " distance=2.03 Simple disulfide: pdb=" SG CYS B2437 " - pdb=" SG CYS B2441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.15 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: 7.09 Time building geometry restraints manager: 3.67 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: 18774 29.99 - 59.99: 729 59.99 - 89.98: 96 89.98 - 119.98: 45 119.98 - 149.97: 42 Dihedral angle restraints: 19686 sinusoidal: 7347 harmonic: 12339 Sorted by residual: dihedral pdb=" CB CYS A1232 " pdb=" SG CYS A1232 " pdb=" SG CYS A1253 " pdb=" CB CYS A1253 " ideal model delta sinusoidal sigma weight residual -86.00 -153.63 67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CB CYS B1232 " pdb=" SG CYS B1232 " pdb=" SG CYS B1253 " pdb=" CB CYS B1253 " ideal model delta sinusoidal sigma weight residual -86.00 -153.60 67.60 1 1.00e+01 1.00e-02 5.94e+01 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 ... (remaining 19683 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: 2.20 - 2.74: 3021 2.74 - 3.28: 32989 3.28 - 3.82: 52837 3.82 - 4.36: 55473 4.36 - 4.90: 97057 Nonbonded interactions: 241377 Sorted by model distance: nonbonded pdb=" N HIS F1300 " pdb=" O P5S F2604 " model vdw 2.205 3.120 nonbonded pdb=" N HIS B1300 " pdb=" O P5S B2604 " model vdw 2.219 3.120 nonbonded pdb=" N HIS A1300 " pdb=" O P5S A2604 " model vdw 2.223 3.120 nonbonded pdb=" CH2 TRP A1717 " pdb=" C8 PLX A2601 " model vdw 2.226 3.740 nonbonded pdb=" CH2 TRP F1717 " pdb=" C8 PLX F2601 " model vdw 2.244 3.740 ... (remaining 241372 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: 0.09 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'B' } 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: 3.460 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 40.080 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- 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 32826 Z= 0.253 Angle : 0.755 14.837 44562 Z= 0.358 Chirality : 0.042 0.387 5166 Planarity : 0.004 0.048 5511 Dihedral : 18.882 149.971 11607 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.000 ARG A1724 TYR 0.011 0.001 TYR F2470 PHE 0.022 0.001 PHE A2062 TRP 0.029 0.002 TRP A 836 HIS 0.006 0.001 HIS A1403 Details of bonding type rmsd covalent geometry : bond 0.00512 (32817) covalent geometry : angle 0.75524 (44544) SS BOND : bond 0.00223 ( 9) SS BOND : angle 0.86601 ( 18) hydrogen bonds : bond 0.11959 ( 2140) hydrogen bonds : angle 5.26395 ( 6363) *********************** 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 : 0.956 Fit side-chains REVERT: F 1152 MET cc_start: 0.8558 (mtt) cc_final: 0.8346 (mtt) REVERT: F 1349 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7573 (mmp) 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: 1 residues processed: 223 average time/residue: 0.1664 time to fit residues: 65.9034 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 : 1.190 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0170 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1304 HIS F2118 ASN F2244 GLN A1304 HIS A2118 ASN A2244 GLN A2435 GLN B1304 HIS B2118 ASN B2244 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067903 restraints weight = 150626.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070421 restraints weight = 68357.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071880 restraints weight = 35583.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071827 restraints weight = 27631.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071947 restraints weight = 24182.277| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32826 Z= 0.123 Angle : 0.573 7.222 44562 Z= 0.292 Chirality : 0.039 0.154 5166 Planarity : 0.004 0.044 5511 Dihedral : 17.672 158.628 5286 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.92 % Allowed : 8.17 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.14), residues: 4104 helix: 1.91 (0.10), residues: 2790 sheet: -0.79 (0.32), residues: 282 loop : -2.62 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F1724 TYR 0.016 0.001 TYR B2470 PHE 0.022 0.001 PHE A2062 TRP 0.022 0.001 TRP A 836 HIS 0.007 0.001 HIS A1403 Details of bonding type rmsd covalent geometry : bond 0.00264 (32817) covalent geometry : angle 0.57288 (44544) SS BOND : bond 0.00234 ( 9) SS BOND : angle 0.64716 ( 18) hydrogen bonds : bond 0.03876 ( 2140) hydrogen bonds : angle 4.23566 ( 6363) *********************** 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 252 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.152 Fit side-chains REVERT: F 1226 MET cc_start: 0.8475 (tpp) cc_final: 0.8200 (mmm) REVERT: F 2053 LEU cc_start: 0.8929 (tp) cc_final: 0.8666 (tp) REVERT: F 2241 MET cc_start: 0.8354 (tpp) cc_final: 0.8143 (tpt) REVERT: A 2031 MET cc_start: 0.8306 (mtm) cc_final: 0.8105 (mtp) REVERT: A 2241 MET cc_start: 0.8358 (tpp) cc_final: 0.8154 (tpt) REVERT: B 1072 MET cc_start: 0.7290 (ptp) cc_final: 0.7052 (ptt) REVERT: B 1238 MET cc_start: 0.6974 (tpp) cc_final: 0.6619 (tpt) REVERT: B 1731 MET cc_start: 0.9019 (tpp) cc_final: 0.8797 (mmp) REVERT: B 2509 ASP cc_start: 0.8202 (m-30) cc_final: 0.7852 (m-30) outliers start: 27 outliers final: 15 residues processed: 235 average time/residue: 0.1610 time to fit residues: 67.6866 Evaluate side-chains 225 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1013 HIS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 153 optimal weight: 0.0370 chunk 247 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2151 ASN F2356 GLN A1225 ASN A2151 ASN A2356 GLN B2151 ASN B2356 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.081222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067516 restraints weight = 155352.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069760 restraints weight = 71090.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071109 restraints weight = 39472.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071012 restraints weight = 32558.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071229 restraints weight = 27004.433| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32826 Z= 0.117 Angle : 0.537 11.702 44562 Z= 0.273 Chirality : 0.038 0.149 5166 Planarity : 0.004 0.035 5511 Dihedral : 16.234 169.743 5277 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.23 % Allowed : 10.09 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.14), residues: 4104 helix: 2.03 (0.10), residues: 2811 sheet: -0.77 (0.32), residues: 276 loop : -2.56 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2098 TYR 0.023 0.001 TYR B1046 PHE 0.018 0.001 PHE A1143 TRP 0.021 0.001 TRP F 836 HIS 0.009 0.001 HIS F1304 Details of bonding type rmsd covalent geometry : bond 0.00259 (32817) covalent geometry : angle 0.53662 (44544) SS BOND : bond 0.00245 ( 9) SS BOND : angle 0.63047 ( 18) hydrogen bonds : bond 0.03556 ( 2140) hydrogen bonds : angle 3.99925 ( 6363) *********************** 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: 36 poor density : 221 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1226 MET cc_start: 0.8509 (tpp) cc_final: 0.8268 (mmm) REVERT: F 2053 LEU cc_start: 0.8891 (tp) cc_final: 0.8651 (tp) REVERT: A 2263 PHE cc_start: 0.8158 (m-80) cc_final: 0.7826 (m-80) REVERT: B 2270 MET cc_start: 0.8038 (mmm) cc_final: 0.7829 (mmm) REVERT: B 2309 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: B 2509 ASP cc_start: 0.8169 (m-30) cc_final: 0.7813 (m-30) outliers start: 36 outliers final: 26 residues processed: 241 average time/residue: 0.1572 time to fit residues: 67.4575 Evaluate side-chains 233 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 1739 VAL Chi-restraints excluded: chain F residue 1791 MET 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 337 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 172 optimal weight: 0.0570 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 409 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 300 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1047 GLN F1225 ASN F2435 GLN A1047 GLN A1304 HIS B1225 ASN ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2435 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.064060 restraints weight = 189315.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066210 restraints weight = 83844.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067719 restraints weight = 45310.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067661 restraints weight = 35538.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067814 restraints weight = 29473.184| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32826 Z= 0.179 Angle : 0.601 10.493 44562 Z= 0.307 Chirality : 0.040 0.165 5166 Planarity : 0.004 0.035 5511 Dihedral : 15.441 164.182 5277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.91 % Allowed : 10.94 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 4104 helix: 2.00 (0.10), residues: 2817 sheet: -0.69 (0.32), residues: 279 loop : -2.63 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2407 TYR 0.024 0.001 TYR B1046 PHE 0.027 0.002 PHE B1143 TRP 0.030 0.002 TRP F 836 HIS 0.011 0.002 HIS F1304 Details of bonding type rmsd covalent geometry : bond 0.00416 (32817) covalent geometry : angle 0.60060 (44544) SS BOND : bond 0.00334 ( 9) SS BOND : angle 0.69759 ( 18) hydrogen bonds : bond 0.04103 ( 2140) hydrogen bonds : angle 4.09385 ( 6363) *********************** 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: 56 poor density : 204 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1009 MET cc_start: 0.7112 (mmm) cc_final: 0.6723 (mmt) REVERT: F 2053 LEU cc_start: 0.8927 (tp) cc_final: 0.8672 (tp) REVERT: A 2263 PHE cc_start: 0.8453 (m-80) cc_final: 0.8076 (m-80) REVERT: B 1238 MET cc_start: 0.7394 (tpt) cc_final: 0.7151 (tpt) REVERT: B 2270 MET cc_start: 0.8142 (mmm) cc_final: 0.7915 (mmm) REVERT: B 2509 ASP cc_start: 0.8222 (m-30) cc_final: 0.7843 (m-30) outliers start: 56 outliers final: 37 residues processed: 239 average time/residue: 0.1574 time to fit residues: 66.4646 Evaluate side-chains 238 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 1312 THR 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 2304 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 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 1739 VAL Chi-restraints excluded: chain A residue 2197 LEU 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 1663 GLU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2304 MET 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 205 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 230 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 270 optimal weight: 0.5980 chunk 7 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1047 GLN ** B1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066094 restraints weight = 129079.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067926 restraints weight = 63337.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069114 restraints weight = 39892.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069927 restraints weight = 29551.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.070440 restraints weight = 24091.529| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32826 Z= 0.112 Angle : 0.525 7.300 44562 Z= 0.271 Chirality : 0.039 0.154 5166 Planarity : 0.003 0.035 5511 Dihedral : 14.993 160.020 5277 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.40 % Allowed : 12.51 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.14), residues: 4104 helix: 2.11 (0.10), residues: 2817 sheet: -0.55 (0.32), residues: 276 loop : -2.56 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2407 TYR 0.021 0.001 TYR B1046 PHE 0.020 0.001 PHE A1143 TRP 0.027 0.001 TRP F 836 HIS 0.007 0.001 HIS F1304 Details of bonding type rmsd covalent geometry : bond 0.00245 (32817) covalent geometry : angle 0.52527 (44544) SS BOND : bond 0.00208 ( 9) SS BOND : angle 0.60510 ( 18) hydrogen bonds : bond 0.03563 ( 2140) hydrogen bonds : angle 3.92668 ( 6363) *********************** 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 243 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2053 LEU cc_start: 0.8872 (tp) cc_final: 0.8612 (tp) REVERT: F 2121 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (tp) REVERT: F 2509 ASP cc_start: 0.8226 (m-30) cc_final: 0.7881 (m-30) REVERT: A 2121 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 2263 PHE cc_start: 0.8186 (m-80) cc_final: 0.7895 (m-80) REVERT: B 2121 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8758 (tp) REVERT: B 2270 MET cc_start: 0.8078 (mmm) cc_final: 0.7869 (mmm) REVERT: B 2408 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 2509 ASP cc_start: 0.8191 (m-30) cc_final: 0.7822 (m-30) outliers start: 41 outliers final: 27 residues processed: 230 average time/residue: 0.1638 time to fit residues: 67.3446 Evaluate side-chains 231 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 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 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 1222 ILE 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 2002 SER 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6215 > 50: distance: 17 - 32: 7.872 distance: 21 - 44: 14.807 distance: 25 - 52: 5.751 distance: 28 - 32: 7.216 distance: 29 - 60: 9.385 distance: 32 - 33: 6.911 distance: 33 - 34: 8.131 distance: 33 - 36: 13.500 distance: 34 - 35: 12.579 distance: 34 - 44: 5.289 distance: 35 - 67: 23.778 distance: 36 - 37: 3.349 distance: 37 - 38: 11.210 distance: 37 - 39: 6.291 distance: 38 - 40: 6.057 distance: 39 - 41: 7.466 distance: 41 - 42: 4.420 distance: 44 - 45: 10.796 distance: 45 - 46: 4.623 distance: 45 - 48: 4.859 distance: 46 - 47: 9.396 distance: 46 - 52: 6.570 distance: 47 - 76: 14.910 distance: 48 - 49: 13.934 distance: 49 - 50: 10.474 distance: 49 - 51: 9.808 distance: 52 - 53: 6.821 distance: 53 - 54: 15.029 distance: 53 - 56: 8.163 distance: 54 - 60: 29.660 distance: 56 - 57: 10.557 distance: 57 - 58: 15.626 distance: 57 - 59: 17.226 distance: 60 - 61: 11.429 distance: 61 - 62: 5.533 distance: 61 - 64: 6.875 distance: 62 - 63: 3.595 distance: 62 - 67: 8.972 distance: 64 - 65: 7.746 distance: 64 - 66: 10.611 distance: 67 - 68: 8.944 distance: 68 - 69: 14.309 distance: 68 - 71: 5.346 distance: 69 - 70: 5.170 distance: 69 - 76: 12.139 distance: 71 - 72: 11.140 distance: 72 - 73: 13.568 distance: 73 - 74: 13.668 distance: 73 - 75: 18.487 distance: 76 - 77: 5.336 distance: 77 - 78: 6.422 distance: 77 - 80: 14.041 distance: 78 - 79: 7.471 distance: 78 - 85: 4.410 distance: 80 - 81: 17.796 distance: 81 - 82: 3.879 distance: 82 - 83: 17.864 distance: 82 - 84: 9.411 distance: 86 - 87: 11.763 distance: 86 - 89: 9.476 distance: 87 - 88: 15.701 distance: 87 - 93: 14.181 distance: 89 - 90: 4.260 distance: 90 - 91: 10.297 distance: 90 - 92: 7.975 distance: 93 - 94: 8.315 distance: 94 - 95: 9.668 distance: 94 - 97: 11.947 distance: 95 - 96: 37.545 distance: 95 - 101: 15.943 distance: 97 - 98: 9.476 distance: 98 - 99: 6.138 distance: 98 - 100: 7.040 distance: 101 - 102: 6.653 distance: 102 - 103: 23.062 distance: 103 - 104: 23.280 distance: 103 - 106: 34.821 distance: 106 - 107: 9.945 distance: 107 - 108: 7.931 distance: 107 - 110: 6.404 distance: 108 - 109: 4.999 distance: 108 - 113: 8.868 distance: 110 - 111: 8.414 distance: 110 - 112: 13.955