Starting phenix.real_space_refine on Wed Mar 4 12:55:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kwo_23057/03_2026/7kwo_23057.map" } resolution = 2.9 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= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 Cu 1 5.60 5 S 114 5.16 5 C 8578 2.51 5 N 2277 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13469 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 9743 Classifications: {'peptide': 1200} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1142} Chain breaks: 12 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3641 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 449} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 1, ' CU': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 310 51.941 110.768 101.763 1.00 19.36 S ATOM 7122 SG CYS A2000 56.263 97.262 88.040 1.00 6.24 S Time building chain proxies: 3.15, per 1000 atoms: 0.23 Number of scatterers: 13469 At special positions: 0 Unit cell: (96.46, 135.68, 152.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 Ca 2 19.99 S 114 16.00 O 2496 8.00 N 2277 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS V 767 " - pdb=" SG CYS V 808 " distance=2.03 Simple disulfide: pdb=" SG CYS V 776 " - pdb=" SG CYS V 804 " distance=2.25 Simple disulfide: pdb=" SG CYS V 788 " - pdb=" SG CYS V 799 " distance=2.04 Simple disulfide: pdb=" SG CYS V 792 " - pdb=" SG CYS V 827 " distance=2.03 Simple disulfide: pdb=" SG CYS V 810 " - pdb=" SG CYS V 821 " distance=2.03 Simple disulfide: pdb=" SG CYS V 829 " - pdb=" SG CYS V 851 " distance=2.03 Simple disulfide: pdb=" SG CYS V 846 " - pdb=" SG CYS V 863 " distance=2.03 Simple disulfide: pdb=" SG CYS V 849 " - pdb=" SG CYS V 858 " distance=2.03 Simple disulfide: pdb=" SG CYS V 867 " - pdb=" SG CYS V 996 " distance=2.03 Simple disulfide: pdb=" SG CYS V 889 " - pdb=" SG CYS V1031 " distance=2.03 Simple disulfide: pdb=" SG CYS V 898 " - pdb=" SG CYS V 993 " distance=2.03 Simple disulfide: pdb=" SG CYS V 914 " - pdb=" SG CYS V 921 " distance=2.03 Simple disulfide: pdb=" SG CYS V1046 " - pdb=" SG CYS V1089 " distance=2.03 Simple disulfide: pdb=" SG CYS V1060 " - pdb=" SG CYS V1084 " distance=2.04 Simple disulfide: pdb=" SG CYS V1071 " - pdb=" SG CYS V1111 " distance=2.03 Simple disulfide: pdb=" SG CYS V1091 " - pdb=" SG CYS V1097 " distance=2.03 Simple disulfide: pdb=" SG CYS V1101 " - pdb=" SG CYS V1126 " distance=2.03 Simple disulfide: pdb=" SG CYS V1130 " - pdb=" SG CYS V1173 " distance=2.03 Simple disulfide: pdb=" SG CYS V1149 " - pdb=" SG CYS V1169 " distance=2.03 Simple disulfide: pdb=" SG CYS V1153 " - pdb=" SG CYS V1165 " distance=2.03 Simple disulfide: pdb=" SG CYS V1157 " - pdb=" SG CYS V1196 " distance=2.03 Simple disulfide: pdb=" SG CYS V1177 " - pdb=" SG CYS V1190 " distance=2.03 Simple disulfide: pdb=" SG CYS V1199 " - pdb=" SG CYS V1227 " distance=2.03 Simple disulfide: pdb=" SG CYS V1222 " - pdb=" SG CYS V1237 " distance=2.03 Simple disulfide: pdb=" SG CYS V1225 " - pdb=" SG CYS V1234 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A2601 " - " ASN A 239 " " NAG A2602 " - " ASN A1810 " " NAG B 1 " - " ASN A2118 " " NAG V1701 " - " ASN V 857 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 348.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2604 " pdb="ZN ZN A2604 " - pdb=" ND1 HIS A 315 " pdb="ZN ZN A2604 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2604 " - pdb=" ND1 HIS A 267 " 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 32 sheets defined 12.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.538A pdb=" N GLY A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 538 through 546 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.539A pdb=" N SER A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 1753 through 1757 removed outlier: 3.804A pdb=" N GLY A1757 " --> pdb=" O GLU A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1844 through 1850 Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1890 through 1899 Processing helix chain 'A' and resid 1912 through 1915 Processing helix chain 'A' and resid 2002 through 2008 Processing helix chain 'A' and resid 2033 through 2035 No H-bonds generated for 'chain 'A' and resid 2033 through 2035' Processing helix chain 'A' and resid 2047 through 2051 Processing helix chain 'A' and resid 2186 through 2188 No H-bonds generated for 'chain 'A' and resid 2186 through 2188' Processing helix chain 'A' and resid 2204 through 2208 Processing helix chain 'V' and resid 825 through 827 No H-bonds generated for 'chain 'V' and resid 825 through 827' Processing helix chain 'V' and resid 917 through 921 removed outlier: 4.124A pdb=" N LYS V 920 " --> pdb=" O PRO V 917 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS V 921 " --> pdb=" O SER V 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 917 through 921' Processing helix chain 'V' and resid 987 through 989 No H-bonds generated for 'chain 'V' and resid 987 through 989' Processing helix chain 'V' and resid 1017 through 1025 removed outlier: 3.874A pdb=" N TRP V1025 " --> pdb=" O PHE V1021 " (cutoff:3.500A) Processing helix chain 'V' and resid 1049 through 1061 Processing helix chain 'V' and resid 1062 through 1065 Processing helix chain 'V' and resid 1068 through 1072 Processing helix chain 'V' and resid 1076 through 1089 removed outlier: 4.589A pdb=" N TYR V1080 " --> pdb=" O ASP V1076 " (cutoff:3.500A) Processing helix chain 'V' and resid 1097 through 1114 removed outlier: 3.651A pdb=" N HIS V1114 " --> pdb=" O VAL V1110 " (cutoff:3.500A) Processing helix chain 'V' and resid 1135 through 1139 removed outlier: 3.734A pdb=" N GLY V1139 " --> pdb=" O ARG V1136 " (cutoff:3.500A) Processing helix chain 'V' and resid 1192 through 1196 removed outlier: 3.706A pdb=" N CYS V1196 " --> pdb=" O PRO V1193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 removed outlier: 5.937A pdb=" N ARG A 3 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 87 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 5 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS A 89 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 7 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 234 removed outlier: 6.825A pdb=" N PHE A 195 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE A 258 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU A 197 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET A 260 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 199 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 431 removed outlier: 4.349A pdb=" N TYR A 385 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP A 382 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 464 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS A 384 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS A 466 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A 386 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 482 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 456 Processing sheet with id=AA8, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.503A pdb=" N SER A 674 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 630 removed outlier: 6.726A pdb=" N LEU A 627 " --> pdb=" O LYS A 707 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER A 709 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 629 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 660 Processing sheet with id=AB2, first strand: chain 'A' and resid 1677 through 1678 Processing sheet with id=AB3, first strand: chain 'A' and resid 1730 through 1737 Processing sheet with id=AB4, first strand: chain 'A' and resid 1763 through 1766 removed outlier: 6.110A pdb=" N ILE A1763 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS A1858 " --> pdb=" O ILE A1763 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A1765 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1917 through 1921 Processing sheet with id=AB6, first strand: chain 'A' and resid 1933 through 1935 Processing sheet with id=AB7, first strand: chain 'A' and resid 1963 through 1966 Processing sheet with id=AB8, first strand: chain 'A' and resid 2023 through 2024 removed outlier: 6.945A pdb=" N CYS A2169 " --> pdb=" O ILE A2081 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE A2081 " --> pdb=" O CYS A2169 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS A2072 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A2150 " --> pdb=" O LYS A2072 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP A2074 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A2148 " --> pdb=" O ASP A2074 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A2076 " --> pdb=" O ALA A2146 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N ALA A2146 " --> pdb=" O LEU A2076 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ILE A2144 " --> pdb=" O PRO A2078 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N ILE A2080 " --> pdb=" O PRO A2142 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N HIS A2082 " --> pdb=" O PHE A2140 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2037 through 2039 removed outlier: 6.716A pdb=" N LYS A2072 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A2150 " --> pdb=" O LYS A2072 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP A2074 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A2148 " --> pdb=" O ASP A2074 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A2076 " --> pdb=" O ALA A2146 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N ALA A2146 " --> pdb=" O LEU A2076 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ILE A2144 " --> pdb=" O PRO A2078 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N ILE A2080 " --> pdb=" O PRO A2142 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N HIS A2082 " --> pdb=" O PHE A2140 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2090 Processing sheet with id=AC2, first strand: chain 'A' and resid 2176 through 2177 removed outlier: 3.827A pdb=" N MET A2176 " --> pdb=" O GLY A2325 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N LEU A2230 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N GLN A2311 " --> pdb=" O LEU A2230 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N VAL A2232 " --> pdb=" O HIS A2309 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N HIS A2309 " --> pdb=" O VAL A2232 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N PHE A2234 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 12.970A pdb=" N ARG A2307 " --> pdb=" O PHE A2234 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A2236 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A2305 " --> pdb=" O LYS A2236 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY A2242 " --> pdb=" O PRO A2299 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N THR A2244 " --> pdb=" O LEU A2297 " (cutoff:3.500A) removed outlier: 11.571A pdb=" N LEU A2297 " --> pdb=" O THR A2244 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N GLN A2246 " --> pdb=" O ASN A2295 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N ASN A2295 " --> pdb=" O GLN A2246 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A2259 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP A2313 " --> pdb=" O VAL A2257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A2257 " --> pdb=" O TRP A2313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2190 through 2192 removed outlier: 12.570A pdb=" N LEU A2230 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N GLN A2311 " --> pdb=" O LEU A2230 " (cutoff:3.500A) removed outlier: 12.509A pdb=" N VAL A2232 " --> pdb=" O HIS A2309 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N HIS A2309 " --> pdb=" O VAL A2232 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N PHE A2234 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 12.970A pdb=" N ARG A2307 " --> pdb=" O PHE A2234 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N LYS A2236 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A2305 " --> pdb=" O LYS A2236 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY A2242 " --> pdb=" O PRO A2299 " (cutoff:3.500A) removed outlier: 11.385A pdb=" N THR A2244 " --> pdb=" O LEU A2297 " (cutoff:3.500A) removed outlier: 11.571A pdb=" N LEU A2297 " --> pdb=" O THR A2244 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N GLN A2246 " --> pdb=" O ASN A2295 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N ASN A2295 " --> pdb=" O GLN A2246 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A2259 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP A2313 " --> pdb=" O VAL A2257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A2257 " --> pdb=" O TRP A2313 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2283 through 2284 Processing sheet with id=AC5, first strand: chain 'A' and resid 2275 through 2276 Processing sheet with id=AC6, first strand: chain 'V' and resid 772 through 774 Processing sheet with id=AC7, first strand: chain 'V' and resid 829 through 831 Processing sheet with id=AC8, first strand: chain 'V' and resid 841 through 844 removed outlier: 3.893A pdb=" N THR V 848 " --> pdb=" O THR V 859 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 882 through 884 removed outlier: 4.084A pdb=" N ILE V 980 " --> pdb=" O THR V 869 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU V 970 " --> pdb=" O LEU V 966 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 890 through 895 removed outlier: 5.901A pdb=" N GLN V 890 " --> pdb=" O ASN V 911 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASN V 911 " --> pdb=" O GLN V 890 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL V 892 " --> pdb=" O VAL V 909 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL V 909 " --> pdb=" O VAL V 892 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU V 933 " --> pdb=" O LYS V 944 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 1143 through 1150 removed outlier: 5.265A pdb=" N TRP V1144 " --> pdb=" O HIS V1176 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS V1176 " --> pdb=" O TRP V1144 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR V1146 " --> pdb=" O HIS V1174 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS V1174 " --> pdb=" O TYR V1146 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER V1148 " --> pdb=" O GLY V1172 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY V1172 " --> pdb=" O SER V1148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 1182 through 1184 Processing sheet with id=AD4, first strand: chain 'V' and resid 1198 through 1201 Processing sheet with id=AD5, first strand: chain 'V' and resid 1211 through 1214 441 hydrogen bonds defined for protein. 1098 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: 2.65 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2433 1.46 - 1.58: 7049 1.58 - 1.70: 1 1.70 - 1.82: 158 Bond restraints: 13818 Sorted by residual: bond pdb=" OH TYS A1680 " pdb=" S TYS A1680 " ideal model delta sigma weight residual 1.679 1.596 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" CZ TYS A1680 " pdb=" OH TYS A1680 " ideal model delta sigma weight residual 1.371 1.435 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N ASP A1676 " pdb=" CA ASP A1676 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.77e+00 bond pdb=" CA THR A2122 " pdb=" C THR A2122 " ideal model delta sigma weight residual 1.522 1.559 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" N GLU V 990 " pdb=" CA GLU V 990 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.19e+00 ... (remaining 13813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 18604 2.66 - 5.33: 128 5.33 - 7.99: 6 7.99 - 10.66: 0 10.66 - 13.32: 1 Bond angle restraints: 18739 Sorted by residual: angle pdb=" N LYS A1967 " pdb=" CA LYS A1967 " pdb=" C LYS A1967 " ideal model delta sigma weight residual 111.96 106.39 5.57 1.41e+00 5.03e-01 1.56e+01 angle pdb=" C LEU A1978 " pdb=" N TYR A1979 " pdb=" CA TYR A1979 " ideal model delta sigma weight residual 121.59 134.91 -13.32 3.54e+00 7.98e-02 1.42e+01 angle pdb=" N THR A2122 " pdb=" CA THR A2122 " pdb=" C THR A2122 " ideal model delta sigma weight residual 112.54 116.76 -4.22 1.22e+00 6.72e-01 1.20e+01 angle pdb=" N MET V 802 " pdb=" CA MET V 802 " pdb=" C MET V 802 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" CA PHE A1677 " pdb=" C PHE A1677 " pdb=" O PHE A1677 " ideal model delta sigma weight residual 121.40 118.03 3.37 1.13e+00 7.83e-01 8.92e+00 ... (remaining 18734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 8095 21.77 - 43.54: 206 43.54 - 65.30: 28 65.30 - 87.07: 11 87.07 - 108.84: 4 Dihedral angle restraints: 8344 sinusoidal: 3465 harmonic: 4879 Sorted by residual: dihedral pdb=" CB CYS V 829 " pdb=" SG CYS V 829 " pdb=" SG CYS V 851 " pdb=" CB CYS V 851 " ideal model delta sinusoidal sigma weight residual -86.00 -127.74 41.74 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" C THR A2122 " pdb=" N THR A2122 " pdb=" CA THR A2122 " pdb=" CB THR A2122 " ideal model delta harmonic sigma weight residual -122.00 -132.02 10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.87 108.84 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1787 0.068 - 0.136: 249 0.136 - 0.204: 7 0.204 - 0.272: 2 0.272 - 0.340: 1 Chirality restraints: 2046 Sorted by residual: chirality pdb=" CA THR A2122 " pdb=" N THR A2122 " pdb=" C THR A2122 " pdb=" CB THR A2122 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL V 805 " pdb=" N VAL V 805 " pdb=" C VAL V 805 " pdb=" CB VAL V 805 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2043 not shown) Planarity restraints: 2389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 805 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C VAL V 805 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL V 805 " -0.012 2.00e-02 2.50e+03 pdb=" N SER V 806 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU V 787 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C GLU V 787 " 0.032 2.00e-02 2.50e+03 pdb=" O GLU V 787 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS V 788 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 82 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ASP A 82 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 82 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 83 " 0.010 2.00e-02 2.50e+03 ... (remaining 2386 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 155 2.61 - 3.19: 11028 3.19 - 3.76: 20545 3.76 - 4.33: 30789 4.33 - 4.90: 50043 Nonbonded interactions: 112560 Sorted by model distance: nonbonded pdb=" ND1 HIS A2005 " pdb="CU CU A2605 " model vdw 2.043 2.320 nonbonded pdb=" OE2 GLU A 389 " pdb=" OH TYR A 431 " model vdw 2.163 3.040 nonbonded pdb=" OD1 ASP A1678 " pdb=" NH1 ARG V 820 " model vdw 2.167 3.120 nonbonded pdb=" OG1 THR V1045 " pdb=" O CYS V1089 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR A1881 " pdb=" O MET A1947 " model vdw 2.198 3.040 ... (remaining 112555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.004 0.219 13859 Z= 0.200 Angle : 0.586 13.325 18821 Z= 0.342 Chirality : 0.046 0.340 2046 Planarity : 0.003 0.030 2385 Dihedral : 10.686 108.841 5106 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.41 (0.20), residues: 1648 helix: 0.22 (0.45), residues: 143 sheet: -0.07 (0.23), residues: 494 loop : -0.38 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 816 TYR 0.017 0.001 TYR A1762 PHE 0.014 0.001 PHE A2014 TRP 0.006 0.001 TRP A2046 HIS 0.003 0.001 HIS A2082 Details of bonding type rmsd covalent geometry : bond 0.00329 (13818) covalent geometry : angle 0.58009 (18739) SS BOND : bond 0.03872 ( 32) SS BOND : angle 1.19439 ( 64) hydrogen bonds : bond 0.11715 ( 414) hydrogen bonds : angle 6.40401 ( 1098) metal coordination : bond 0.00168 ( 3) link_BETA1-4 : bond 0.00539 ( 2) link_BETA1-4 : angle 2.42576 ( 6) link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 1.74566 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 0.5809 time to fit residues: 88.0373 Evaluate side-chains 77 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 966 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.117113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078838 restraints weight = 29881.738| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.90 r_work: 0.3340 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13859 Z= 0.126 Angle : 0.546 8.453 18821 Z= 0.280 Chirality : 0.044 0.155 2046 Planarity : 0.004 0.033 2385 Dihedral : 7.254 75.055 1936 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.35 % Allowed : 9.35 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.25 (0.21), residues: 1648 helix: 0.20 (0.43), residues: 145 sheet: 0.08 (0.24), residues: 478 loop : -0.28 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V1035 TYR 0.015 0.001 TYR A 532 PHE 0.018 0.001 PHE V1100 TRP 0.007 0.001 TRP V1120 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00288 (13818) covalent geometry : angle 0.53642 (18739) SS BOND : bond 0.00272 ( 32) SS BOND : angle 1.43384 ( 64) hydrogen bonds : bond 0.03216 ( 414) hydrogen bonds : angle 5.51597 ( 1098) metal coordination : bond 0.00155 ( 3) link_BETA1-4 : bond 0.00479 ( 2) link_BETA1-4 : angle 2.76871 ( 6) link_NAG-ASN : bond 0.00125 ( 4) link_NAG-ASN : angle 1.74081 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8402 (t0) cc_final: 0.8182 (t0) REVERT: A 478 HIS cc_start: 0.8057 (m-70) cc_final: 0.7312 (m170) REVERT: A 2055 TYR cc_start: 0.7914 (t80) cc_final: 0.7482 (t80) REVERT: V 927 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9049 (pp) outliers start: 20 outliers final: 6 residues processed: 93 average time/residue: 0.5155 time to fit residues: 53.4810 Evaluate side-chains 81 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 0.0000 chunk 100 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 478 HIS V1069 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.114179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.075756 restraints weight = 30512.667| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.87 r_work: 0.3277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13859 Z= 0.223 Angle : 0.585 8.693 18821 Z= 0.301 Chirality : 0.045 0.152 2046 Planarity : 0.004 0.038 2385 Dihedral : 6.451 55.923 1934 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 10.09 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.30 (0.21), residues: 1648 helix: 0.23 (0.43), residues: 145 sheet: 0.01 (0.24), residues: 486 loop : -0.30 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2320 TYR 0.020 0.002 TYR A1762 PHE 0.020 0.002 PHE V1100 TRP 0.010 0.001 TRP V1120 HIS 0.005 0.001 HIS A1919 Details of bonding type rmsd covalent geometry : bond 0.00513 (13818) covalent geometry : angle 0.57704 (18739) SS BOND : bond 0.00272 ( 32) SS BOND : angle 1.15656 ( 64) hydrogen bonds : bond 0.03192 ( 414) hydrogen bonds : angle 5.57679 ( 1098) metal coordination : bond 0.00431 ( 3) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 3.51905 ( 6) link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 1.73895 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: A 251 LYS cc_start: 0.8862 (mptt) cc_final: 0.8623 (mptt) REVERT: A 440 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: A 478 HIS cc_start: 0.8176 (m90) cc_final: 0.7369 (m170) REVERT: A 539 MET cc_start: 0.8727 (mpt) cc_final: 0.8470 (mpp) REVERT: A 2055 TYR cc_start: 0.8130 (t80) cc_final: 0.7614 (t80) REVERT: V 927 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9067 (pp) REVERT: V 934 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8306 (mm) REVERT: V 947 MET cc_start: 0.2333 (mmp) cc_final: 0.0744 (mpm) outliers start: 34 outliers final: 11 residues processed: 102 average time/residue: 0.5041 time to fit residues: 57.2732 Evaluate side-chains 89 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 928 LEU Chi-restraints excluded: chain V residue 934 ILE Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 10 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** 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 = 0.4164 r_free = 0.4164 target = 0.113906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075704 restraints weight = 30160.065| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.81 r_work: 0.3278 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13859 Z= 0.202 Angle : 0.570 6.965 18821 Z= 0.294 Chirality : 0.045 0.160 2046 Planarity : 0.004 0.033 2385 Dihedral : 5.932 55.325 1934 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.42 % Allowed : 10.97 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.34 (0.21), residues: 1648 helix: 0.19 (0.43), residues: 145 sheet: -0.03 (0.24), residues: 483 loop : -0.32 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1941 TYR 0.017 0.002 TYR A1976 PHE 0.019 0.001 PHE V1100 TRP 0.012 0.001 TRP V1120 HIS 0.005 0.001 HIS V 831 Details of bonding type rmsd covalent geometry : bond 0.00460 (13818) covalent geometry : angle 0.56229 (18739) SS BOND : bond 0.00262 ( 32) SS BOND : angle 1.21624 ( 64) hydrogen bonds : bond 0.03085 ( 414) hydrogen bonds : angle 5.50340 ( 1098) metal coordination : bond 0.00365 ( 3) link_BETA1-4 : bond 0.00240 ( 2) link_BETA1-4 : angle 3.17813 ( 6) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 1.76950 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: A 147 MET cc_start: 0.7956 (mmm) cc_final: 0.7683 (mtt) REVERT: A 251 LYS cc_start: 0.8835 (mptt) cc_final: 0.8562 (mptt) REVERT: A 400 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 478 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7405 (m170) REVERT: A 539 MET cc_start: 0.8736 (mpt) cc_final: 0.8495 (mpp) REVERT: A 2055 TYR cc_start: 0.8109 (t80) cc_final: 0.7530 (t80) REVERT: V 927 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9075 (pp) outliers start: 36 outliers final: 12 residues processed: 97 average time/residue: 0.5118 time to fit residues: 55.2102 Evaluate side-chains 90 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 1149 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 161 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** 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 = 0.4184 r_free = 0.4184 target = 0.115170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077069 restraints weight = 30088.911| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.81 r_work: 0.3309 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13859 Z= 0.123 Angle : 0.535 8.570 18821 Z= 0.273 Chirality : 0.044 0.171 2046 Planarity : 0.003 0.032 2385 Dihedral : 5.474 54.705 1934 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.56 % Allowed : 11.17 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.24 (0.21), residues: 1648 helix: 0.27 (0.44), residues: 145 sheet: 0.05 (0.24), residues: 485 loop : -0.26 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2209 TYR 0.012 0.001 TYR A1976 PHE 0.020 0.001 PHE A 501 TRP 0.014 0.001 TRP V1120 HIS 0.007 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00279 (13818) covalent geometry : angle 0.52811 (18739) SS BOND : bond 0.00369 ( 32) SS BOND : angle 1.18806 ( 64) hydrogen bonds : bond 0.02825 ( 414) hydrogen bonds : angle 5.32286 ( 1098) metal coordination : bond 0.00165 ( 3) link_BETA1-4 : bond 0.00332 ( 2) link_BETA1-4 : angle 2.70065 ( 6) link_NAG-ASN : bond 0.00168 ( 4) link_NAG-ASN : angle 1.74455 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 127 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8176 (mtpm) REVERT: A 147 MET cc_start: 0.7926 (mmm) cc_final: 0.7718 (mtt) REVERT: A 251 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8531 (mptt) REVERT: A 440 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 478 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7425 (m170) REVERT: A 682 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8582 (mmm) REVERT: A 2055 TYR cc_start: 0.8113 (t80) cc_final: 0.7571 (t80) REVERT: A 2199 MET cc_start: 0.7319 (ptp) cc_final: 0.7074 (ppp) REVERT: V 872 MET cc_start: 0.5438 (pmm) cc_final: 0.5215 (pmm) REVERT: V 927 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9049 (pp) REVERT: V 934 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8151 (mp) REVERT: V 1116 LYS cc_start: 0.3696 (OUTLIER) cc_final: 0.3476 (pttp) outliers start: 38 outliers final: 13 residues processed: 101 average time/residue: 0.5278 time to fit residues: 59.4882 Evaluate side-chains 98 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 800 MET Chi-restraints excluded: chain V residue 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 934 ILE Chi-restraints excluded: chain V residue 1116 LYS Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 0.0270 chunk 31 optimal weight: 4.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.113427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075005 restraints weight = 30281.425| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.89 r_work: 0.3267 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13859 Z= 0.228 Angle : 0.581 9.049 18821 Z= 0.297 Chirality : 0.045 0.156 2046 Planarity : 0.004 0.033 2385 Dihedral : 5.554 55.875 1934 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.96 % Allowed : 11.31 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.40 (0.21), residues: 1648 helix: 0.22 (0.43), residues: 145 sheet: -0.11 (0.23), residues: 497 loop : -0.36 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.017 0.002 TYR A2105 PHE 0.018 0.002 PHE V1100 TRP 0.014 0.001 TRP V1120 HIS 0.009 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00523 (13818) covalent geometry : angle 0.57505 (18739) SS BOND : bond 0.00257 ( 32) SS BOND : angle 1.01948 ( 64) hydrogen bonds : bond 0.03044 ( 414) hydrogen bonds : angle 5.47520 ( 1098) metal coordination : bond 0.00378 ( 3) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 2.79111 ( 6) link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 1.74826 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: A 84 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 127 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (mtpm) REVERT: A 251 LYS cc_start: 0.8821 (mptt) cc_final: 0.8493 (mptt) REVERT: A 299 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8685 (tm) REVERT: A 400 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 440 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 478 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7456 (m170) REVERT: A 682 MET cc_start: 0.9181 (mpt) cc_final: 0.8947 (mmt) REVERT: A 2055 TYR cc_start: 0.8111 (t80) cc_final: 0.7509 (t80) REVERT: A 2199 MET cc_start: 0.7343 (ptp) cc_final: 0.7091 (ppp) REVERT: V 927 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9099 (pp) REVERT: V 934 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 44 outliers final: 16 residues processed: 102 average time/residue: 0.5180 time to fit residues: 58.7999 Evaluate side-chains 98 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 934 ILE Chi-restraints excluded: chain V residue 1029 SER Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 57 optimal weight: 3.9990 chunk 142 optimal weight: 0.0050 chunk 85 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.115483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077532 restraints weight = 29951.533| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.83 r_work: 0.3325 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13859 Z= 0.104 Angle : 0.534 10.237 18821 Z= 0.269 Chirality : 0.044 0.153 2046 Planarity : 0.003 0.031 2385 Dihedral : 5.157 54.534 1934 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.36 % Allowed : 11.91 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.18 (0.21), residues: 1648 helix: 0.38 (0.44), residues: 145 sheet: 0.02 (0.23), residues: 507 loop : -0.20 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 820 TYR 0.010 0.001 TYR A2148 PHE 0.020 0.001 PHE A 501 TRP 0.010 0.001 TRP A2062 HIS 0.008 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00236 (13818) covalent geometry : angle 0.52939 (18739) SS BOND : bond 0.00179 ( 32) SS BOND : angle 0.87526 ( 64) hydrogen bonds : bond 0.02659 ( 414) hydrogen bonds : angle 5.23861 ( 1098) metal coordination : bond 0.00160 ( 3) link_BETA1-4 : bond 0.00326 ( 2) link_BETA1-4 : angle 1.98476 ( 6) link_NAG-ASN : bond 0.00141 ( 4) link_NAG-ASN : angle 1.67977 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 127 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8165 (mtpm) REVERT: A 251 LYS cc_start: 0.8751 (mptt) cc_final: 0.8496 (mptt) REVERT: A 299 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8760 (tm) REVERT: A 440 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 478 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7489 (m170) REVERT: A 539 MET cc_start: 0.8694 (mpt) cc_final: 0.8469 (mpp) REVERT: A 682 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8830 (mmt) REVERT: A 2055 TYR cc_start: 0.8081 (t80) cc_final: 0.7617 (t80) REVERT: A 2064 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9144 (p) REVERT: A 2199 MET cc_start: 0.7329 (ptp) cc_final: 0.6947 (ppp) REVERT: V 771 MET cc_start: 0.7641 (mmp) cc_final: 0.7324 (mmm) REVERT: V 872 MET cc_start: 0.5498 (pmm) cc_final: 0.5208 (pmm) REVERT: V 927 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9095 (pp) REVERT: V 934 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8136 (mp) REVERT: V 1016 GLU cc_start: 0.8563 (mp0) cc_final: 0.8009 (tm-30) outliers start: 35 outliers final: 9 residues processed: 106 average time/residue: 0.5041 time to fit residues: 59.7862 Evaluate side-chains 91 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 934 ILE Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 121 optimal weight: 0.0050 chunk 85 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.115093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077689 restraints weight = 29544.725| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.73 r_work: 0.3322 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13859 Z= 0.121 Angle : 0.541 11.164 18821 Z= 0.271 Chirality : 0.044 0.148 2046 Planarity : 0.003 0.030 2385 Dihedral : 5.148 54.727 1934 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.22 % Allowed : 12.25 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.14 (0.21), residues: 1648 helix: 0.31 (0.44), residues: 145 sheet: 0.16 (0.24), residues: 494 loop : -0.22 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1897 TYR 0.012 0.001 TYR A 636 PHE 0.019 0.001 PHE V1100 TRP 0.018 0.001 TRP V1120 HIS 0.011 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00275 (13818) covalent geometry : angle 0.53520 (18739) SS BOND : bond 0.00176 ( 32) SS BOND : angle 1.12051 ( 64) hydrogen bonds : bond 0.02803 ( 414) hydrogen bonds : angle 5.20349 ( 1098) metal coordination : bond 0.00162 ( 3) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 2.02948 ( 6) link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 1.69121 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8209 (mtpm) REVERT: A 251 LYS cc_start: 0.8776 (mptt) cc_final: 0.8515 (mptt) REVERT: A 299 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8720 (tm) REVERT: A 478 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7460 (m170) REVERT: A 682 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8704 (mmm) REVERT: A 2055 TYR cc_start: 0.8116 (t80) cc_final: 0.7581 (t80) REVERT: A 2199 MET cc_start: 0.7354 (ptp) cc_final: 0.6980 (ppp) REVERT: V 872 MET cc_start: 0.5529 (pmm) cc_final: 0.5268 (pmm) REVERT: V 927 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9084 (pp) REVERT: V 934 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8116 (mp) REVERT: V 1016 GLU cc_start: 0.8555 (mp0) cc_final: 0.7980 (tm-30) REVERT: V 1076 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6211 (p0) outliers start: 33 outliers final: 11 residues processed: 100 average time/residue: 0.5332 time to fit residues: 59.3362 Evaluate side-chains 92 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 934 ILE Chi-restraints excluded: chain V residue 1076 ASP Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A2315 HIS ** V 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076005 restraints weight = 29979.180| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.72 r_work: 0.3282 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13859 Z= 0.203 Angle : 0.593 11.814 18821 Z= 0.299 Chirality : 0.045 0.167 2046 Planarity : 0.004 0.035 2385 Dihedral : 5.371 55.751 1934 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.88 % Allowed : 12.65 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.29 (0.21), residues: 1648 helix: 0.31 (0.44), residues: 145 sheet: 0.08 (0.24), residues: 472 loop : -0.35 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 439 TYR 0.016 0.002 TYR A2105 PHE 0.024 0.002 PHE A 501 TRP 0.019 0.001 TRP V1120 HIS 0.012 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00463 (13818) covalent geometry : angle 0.58872 (18739) SS BOND : bond 0.00236 ( 32) SS BOND : angle 1.01523 ( 64) hydrogen bonds : bond 0.03018 ( 414) hydrogen bonds : angle 5.38622 ( 1098) metal coordination : bond 0.00310 ( 3) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 2.23350 ( 6) link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 1.77619 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8307 (mtpm) REVERT: A 251 LYS cc_start: 0.8794 (mptt) cc_final: 0.8514 (mptt) REVERT: A 299 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8628 (tm) REVERT: A 478 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7474 (m170) REVERT: A 682 MET cc_start: 0.9172 (mpt) cc_final: 0.8912 (mmt) REVERT: A 2055 TYR cc_start: 0.8093 (t80) cc_final: 0.7513 (t80) REVERT: A 2199 MET cc_start: 0.7356 (ptp) cc_final: 0.7088 (ppp) REVERT: A 2255 MET cc_start: 0.5378 (tpp) cc_final: 0.3998 (mpp) REVERT: V 927 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9103 (pp) REVERT: V 1076 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6039 (p0) outliers start: 28 outliers final: 14 residues processed: 95 average time/residue: 0.5493 time to fit residues: 57.9388 Evaluate side-chains 92 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 842 VAL Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 1029 SER Chi-restraints excluded: chain V residue 1062 ILE Chi-restraints excluded: chain V residue 1076 ASP Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 158 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** V 831 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 = 0.4174 r_free = 0.4174 target = 0.114293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076620 restraints weight = 29758.284| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.79 r_work: 0.3300 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13859 Z= 0.149 Angle : 0.574 12.303 18821 Z= 0.286 Chirality : 0.045 0.152 2046 Planarity : 0.004 0.035 2385 Dihedral : 5.281 55.503 1934 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.35 % Allowed : 13.32 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.29 (0.21), residues: 1648 helix: 0.29 (0.43), residues: 145 sheet: -0.00 (0.24), residues: 488 loop : -0.29 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 439 TYR 0.012 0.001 TYR A2148 PHE 0.019 0.001 PHE V1100 TRP 0.015 0.001 TRP V1120 HIS 0.011 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00341 (13818) covalent geometry : angle 0.56983 (18739) SS BOND : bond 0.00197 ( 32) SS BOND : angle 0.90503 ( 64) hydrogen bonds : bond 0.02876 ( 414) hydrogen bonds : angle 5.30587 ( 1098) metal coordination : bond 0.00205 ( 3) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 1.93666 ( 6) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 1.81155 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7286 (mmm) cc_final: 0.7047 (mmt) REVERT: A 127 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8290 (mtpm) REVERT: A 251 LYS cc_start: 0.8799 (mptt) cc_final: 0.8529 (mptt) REVERT: A 299 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (tm) REVERT: A 478 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7467 (m170) REVERT: A 682 MET cc_start: 0.9187 (mpt) cc_final: 0.8932 (mmt) REVERT: A 2055 TYR cc_start: 0.8116 (t80) cc_final: 0.7582 (t80) REVERT: A 2092 LYS cc_start: 0.8701 (pttp) cc_final: 0.8469 (ptmm) REVERT: A 2255 MET cc_start: 0.5340 (tpp) cc_final: 0.3923 (mpp) REVERT: V 771 MET cc_start: 0.7565 (mmp) cc_final: 0.7269 (mmm) REVERT: V 927 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9110 (pp) REVERT: V 1016 GLU cc_start: 0.8574 (mp0) cc_final: 0.7996 (tm-30) REVERT: V 1076 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6281 (p0) outliers start: 20 outliers final: 11 residues processed: 90 average time/residue: 0.5704 time to fit residues: 56.8399 Evaluate side-chains 91 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 1076 ASP Chi-restraints excluded: chain V residue 1149 CYS Chi-restraints excluded: chain V residue 1201 VAL Chi-restraints excluded: chain V residue 1230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 102 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2082 HIS ** A2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2295 ASN A2315 HIS ** V 831 HIS ** 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 = 0.4153 r_free = 0.4153 target = 0.113004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075291 restraints weight = 29972.255| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.78 r_work: 0.3269 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13859 Z= 0.226 Angle : 0.618 12.005 18821 Z= 0.310 Chirality : 0.045 0.138 2046 Planarity : 0.004 0.036 2385 Dihedral : 5.499 56.321 1934 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 13.12 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.44 (0.21), residues: 1648 helix: 0.28 (0.44), residues: 144 sheet: -0.13 (0.23), residues: 497 loop : -0.40 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 439 TYR 0.016 0.002 TYR A1976 PHE 0.026 0.002 PHE A 501 TRP 0.013 0.001 TRP V1120 HIS 0.012 0.001 HIS A2315 Details of bonding type rmsd covalent geometry : bond 0.00516 (13818) covalent geometry : angle 0.61395 (18739) SS BOND : bond 0.00253 ( 32) SS BOND : angle 0.95163 ( 64) hydrogen bonds : bond 0.03122 ( 414) hydrogen bonds : angle 5.47932 ( 1098) metal coordination : bond 0.00415 ( 3) link_BETA1-4 : bond 0.00295 ( 2) link_BETA1-4 : angle 2.15063 ( 6) link_NAG-ASN : bond 0.00424 ( 4) link_NAG-ASN : angle 1.90334 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6481.82 seconds wall clock time: 110 minutes 34.12 seconds (6634.12 seconds total)