Starting phenix.real_space_refine on Thu Jul 31 19:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_23057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_23057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_23057.map" model { file = "/net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_23057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kwo_23057/07_2025/7kwo_23057.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG: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: 8.63, per 1000 atoms: 0.64 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.24 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: 7.22 Time building geometry restraints manager: 3.94 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (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 TRP 0.006 0.001 TRP A2046 HIS 0.003 0.001 HIS A2082 PHE 0.014 0.001 PHE A2014 TYR 0.017 0.001 TYR A1762 ARG 0.005 0.000 ARG V 816 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 4) link_NAG-ASN : angle 1.74566 ( 12) link_BETA1-4 : bond 0.00539 ( 2) link_BETA1-4 : angle 2.42576 ( 6) hydrogen bonds : bond 0.11715 ( 414) hydrogen bonds : angle 6.40401 ( 1098) metal coordination : bond 0.00168 ( 3) SS BOND : bond 0.03872 ( 32) SS BOND : angle 1.19439 ( 64) covalent geometry : bond 0.00329 (13818) covalent geometry : angle 0.58009 (18739) *********************** 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 : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 1.2591 time to fit residues: 191.9171 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 : 1.462 ------------------------------------------------------------------------------- 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 141 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 311 HIS A 468 GLN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 ASN A2284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.114658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076227 restraints weight = 30128.498| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.83 r_work: 0.3282 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13859 Z= 0.242 Angle : 0.611 8.345 18821 Z= 0.314 Chirality : 0.045 0.148 2046 Planarity : 0.004 0.037 2385 Dihedral : 7.496 76.632 1936 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.82 % Allowed : 9.15 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1648 helix: 0.13 (0.43), residues: 145 sheet: 0.01 (0.24), residues: 481 loop : -0.37 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1817 HIS 0.006 0.001 HIS A 478 PHE 0.018 0.002 PHE V1100 TYR 0.019 0.002 TYR A1762 ARG 0.007 0.001 ARG V1035 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 4) link_NAG-ASN : angle 1.79414 ( 12) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 3.05928 ( 6) hydrogen bonds : bond 0.03382 ( 414) hydrogen bonds : angle 5.64961 ( 1098) metal coordination : bond 0.00387 ( 3) SS BOND : bond 0.00291 ( 32) SS BOND : angle 1.47737 ( 64) covalent geometry : bond 0.00554 (13818) covalent geometry : angle 0.60157 (18739) *********************** 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 108 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: A 478 HIS cc_start: 0.8128 (m-70) cc_final: 0.7379 (m170) REVERT: V 927 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9065 (pp) REVERT: V 947 MET cc_start: 0.3320 (mmp) cc_final: 0.2560 (mpm) REVERT: V 1073 LYS cc_start: 0.9196 (mttt) cc_final: 0.8930 (mmtt) outliers start: 27 outliers final: 9 residues processed: 98 average time/residue: 1.1304 time to fit residues: 124.0683 Evaluate side-chains 83 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 V residue 927 ILE Chi-restraints excluded: chain V residue 928 LEU 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 17 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 847 ASN V1069 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.114808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076549 restraints weight = 30222.497| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.87 r_work: 0.3291 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13859 Z= 0.168 Angle : 0.553 8.200 18821 Z= 0.284 Chirality : 0.044 0.144 2046 Planarity : 0.004 0.030 2385 Dihedral : 6.499 56.671 1934 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 10.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1648 helix: 0.20 (0.43), residues: 145 sheet: 0.05 (0.24), residues: 482 loop : -0.32 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V1120 HIS 0.004 0.001 HIS A 311 PHE 0.020 0.001 PHE V1100 TYR 0.016 0.001 TYR A1762 ARG 0.003 0.000 ARG A2320 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 4) link_NAG-ASN : angle 1.72338 ( 12) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 3.19443 ( 6) hydrogen bonds : bond 0.03019 ( 414) hydrogen bonds : angle 5.50209 ( 1098) metal coordination : bond 0.00277 ( 3) SS BOND : bond 0.00250 ( 32) SS BOND : angle 0.98562 ( 64) covalent geometry : bond 0.00385 (13818) covalent geometry : angle 0.54697 (18739) *********************** 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 107 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: A 251 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8598 (mptt) REVERT: A 440 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 478 HIS cc_start: 0.8212 (m-70) cc_final: 0.7442 (m170) REVERT: A 539 MET cc_start: 0.8747 (mpt) cc_final: 0.8528 (mpp) REVERT: A 2055 TYR cc_start: 0.8074 (t80) cc_final: 0.7498 (t80) REVERT: V 927 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9059 (pp) REVERT: V 947 MET cc_start: 0.3248 (OUTLIER) cc_final: 0.2444 (mpm) REVERT: V 1116 LYS cc_start: 0.3624 (OUTLIER) cc_final: 0.3365 (pttp) outliers start: 32 outliers final: 10 residues processed: 91 average time/residue: 1.2659 time to fit residues: 128.0371 Evaluate side-chains 87 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 251 LYS 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 1947 MET 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 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET Chi-restraints excluded: chain V residue 1116 LYS 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 73 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- 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 ** A1919 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 = 0.4154 r_free = 0.4154 target = 0.113319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074956 restraints weight = 29952.462| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.85 r_work: 0.3265 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13859 Z= 0.231 Angle : 0.593 8.567 18821 Z= 0.305 Chirality : 0.045 0.171 2046 Planarity : 0.004 0.033 2385 Dihedral : 6.023 55.692 1934 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.62 % Allowed : 10.70 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1648 helix: 0.14 (0.43), residues: 145 sheet: -0.15 (0.24), residues: 489 loop : -0.37 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V1120 HIS 0.005 0.001 HIS V 831 PHE 0.019 0.002 PHE V1100 TYR 0.018 0.002 TYR A1762 ARG 0.002 0.000 ARG A1941 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 4) link_NAG-ASN : angle 1.78370 ( 12) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 3.37868 ( 6) hydrogen bonds : bond 0.03165 ( 414) hydrogen bonds : angle 5.55452 ( 1098) metal coordination : bond 0.00397 ( 3) SS BOND : bond 0.00274 ( 32) SS BOND : angle 1.22571 ( 64) covalent geometry : bond 0.00527 (13818) covalent geometry : angle 0.58483 (18739) *********************** 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 116 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8345 (mmm) REVERT: A 147 MET cc_start: 0.8001 (mmm) cc_final: 0.7717 (mtt) REVERT: A 251 LYS cc_start: 0.8821 (mptt) cc_final: 0.8559 (mptt) REVERT: A 299 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8495 (tm) REVERT: A 478 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7301 (m170) REVERT: A 539 MET cc_start: 0.8761 (mpt) cc_final: 0.8530 (mpp) REVERT: A 2055 TYR cc_start: 0.8122 (t80) cc_final: 0.7476 (t80) REVERT: V 927 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9079 (pp) REVERT: V 947 MET cc_start: 0.3203 (OUTLIER) cc_final: 0.2399 (mpm) outliers start: 39 outliers final: 13 residues processed: 100 average time/residue: 1.1326 time to fit residues: 127.1887 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 : 1.639 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 317 HIS 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 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET 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 156 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.114676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076512 restraints weight = 29873.135| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.78 r_work: 0.3295 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13859 Z= 0.131 Angle : 0.546 8.489 18821 Z= 0.280 Chirality : 0.044 0.164 2046 Planarity : 0.003 0.031 2385 Dihedral : 5.620 55.170 1934 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.69 % Allowed : 11.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1648 helix: 0.24 (0.44), residues: 145 sheet: -0.05 (0.24), residues: 483 loop : -0.30 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V1120 HIS 0.008 0.001 HIS A2315 PHE 0.020 0.001 PHE A 501 TYR 0.014 0.001 TYR A 532 ARG 0.005 0.000 ARG V1035 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 4) link_NAG-ASN : angle 1.77338 ( 12) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 2.80492 ( 6) hydrogen bonds : bond 0.02832 ( 414) hydrogen bonds : angle 5.44900 ( 1098) metal coordination : bond 0.00191 ( 3) SS BOND : bond 0.00276 ( 32) SS BOND : angle 1.14825 ( 64) covalent geometry : bond 0.00299 (13818) covalent geometry : angle 0.53839 (18739) *********************** 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: 40 poor density : 76 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: A 84 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 127 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (mtpm) REVERT: A 147 MET cc_start: 0.7971 (mmm) cc_final: 0.7700 (mtt) REVERT: A 251 LYS cc_start: 0.8813 (mptt) cc_final: 0.8564 (mptt) REVERT: A 440 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 478 HIS cc_start: 0.7957 (m-70) cc_final: 0.7619 (m170) REVERT: A 2055 TYR cc_start: 0.8119 (t80) cc_final: 0.7520 (t80) REVERT: V 872 MET cc_start: 0.5625 (pmm) cc_final: 0.5379 (pmm) REVERT: V 927 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9101 (pp) REVERT: V 947 MET cc_start: 0.3086 (OUTLIER) cc_final: 0.2247 (mpm) outliers start: 40 outliers final: 14 residues processed: 103 average time/residue: 1.1140 time to fit residues: 128.2993 Evaluate side-chains 94 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 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 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 947 MET Chi-restraints excluded: chain V residue 1029 SER 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 1 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 478 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.112760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074255 restraints weight = 30471.524| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.89 r_work: 0.3252 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13859 Z= 0.256 Angle : 0.614 9.234 18821 Z= 0.313 Chirality : 0.046 0.149 2046 Planarity : 0.004 0.034 2385 Dihedral : 5.696 56.108 1934 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 11.78 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1648 helix: 0.18 (0.43), residues: 145 sheet: -0.21 (0.23), residues: 509 loop : -0.40 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP V1120 HIS 0.010 0.001 HIS A2315 PHE 0.018 0.002 PHE V1100 TYR 0.022 0.002 TYR A1976 ARG 0.002 0.000 ARG A2320 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 1.78999 ( 12) link_BETA1-4 : bond 0.00309 ( 2) link_BETA1-4 : angle 2.94111 ( 6) hydrogen bonds : bond 0.03137 ( 414) hydrogen bonds : angle 5.62013 ( 1098) metal coordination : bond 0.00412 ( 3) SS BOND : bond 0.00290 ( 32) SS BOND : angle 1.05547 ( 64) covalent geometry : bond 0.00587 (13818) covalent geometry : angle 0.60861 (18739) *********************** 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 114 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8421 (mmm) REVERT: A 84 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 127 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8347 (mtpm) REVERT: A 251 LYS cc_start: 0.8851 (mptt) cc_final: 0.8577 (mptt) REVERT: A 429 MET cc_start: 0.7507 (mpp) cc_final: 0.5929 (mtt) REVERT: A 439 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (mtp85) REVERT: A 478 HIS cc_start: 0.8293 (m90) cc_final: 0.7512 (m170) REVERT: A 497 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 2055 TYR cc_start: 0.8142 (t80) cc_final: 0.7574 (t80) REVERT: V 927 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9101 (pp) REVERT: V 947 MET cc_start: 0.3124 (OUTLIER) cc_final: 0.2332 (mpm) REVERT: V 1073 LYS cc_start: 0.9225 (mttt) cc_final: 0.8849 (pptt) outliers start: 38 outliers final: 17 residues processed: 101 average time/residue: 1.5633 time to fit residues: 176.7068 Evaluate side-chains 98 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 317 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 497 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 2248 VAL 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 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET 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 137 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 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 = 0.4158 r_free = 0.4158 target = 0.113458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075328 restraints weight = 29994.108| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.76 r_work: 0.3271 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13859 Z= 0.183 Angle : 0.575 10.378 18821 Z= 0.293 Chirality : 0.045 0.147 2046 Planarity : 0.004 0.033 2385 Dihedral : 5.514 55.517 1934 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.76 % Allowed : 11.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1648 helix: 0.26 (0.44), residues: 145 sheet: -0.19 (0.23), residues: 503 loop : -0.37 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V1120 HIS 0.010 0.001 HIS A2315 PHE 0.022 0.002 PHE A 501 TYR 0.013 0.001 TYR A 511 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 4) link_NAG-ASN : angle 1.75873 ( 12) link_BETA1-4 : bond 0.00259 ( 2) link_BETA1-4 : angle 2.32410 ( 6) hydrogen bonds : bond 0.02932 ( 414) hydrogen bonds : angle 5.52594 ( 1098) metal coordination : bond 0.00341 ( 3) SS BOND : bond 0.00232 ( 32) SS BOND : angle 0.98984 ( 64) covalent geometry : bond 0.00416 (13818) covalent geometry : angle 0.56976 (18739) *********************** 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 118 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: A 84 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 127 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8253 (mtpm) REVERT: A 251 LYS cc_start: 0.8809 (mptt) cc_final: 0.8497 (mptt) REVERT: A 299 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8487 (tm) REVERT: A 429 MET cc_start: 0.7459 (mpp) cc_final: 0.6081 (mtt) REVERT: A 478 HIS cc_start: 0.8199 (m90) cc_final: 0.7457 (m170) REVERT: A 497 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7655 (p90) REVERT: A 539 MET cc_start: 0.8751 (mpt) cc_final: 0.8516 (mpp) REVERT: A 2055 TYR cc_start: 0.8143 (t80) cc_final: 0.7580 (t80) REVERT: V 872 MET cc_start: 0.5834 (pmm) cc_final: 0.5473 (pmm) REVERT: V 927 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9129 (pp) REVERT: V 947 MET cc_start: 0.3038 (OUTLIER) cc_final: 0.2246 (mpm) REVERT: V 1073 LYS cc_start: 0.9217 (mttt) cc_final: 0.8827 (pptt) outliers start: 41 outliers final: 21 residues processed: 109 average time/residue: 1.1106 time to fit residues: 136.9796 Evaluate side-chains 101 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 497 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2038 THR 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 2248 VAL 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 846 CYS Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET 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 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 108 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 249 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.113822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075600 restraints weight = 30091.757| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.78 r_work: 0.3279 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13859 Z= 0.167 Angle : 0.585 11.128 18821 Z= 0.297 Chirality : 0.045 0.148 2046 Planarity : 0.004 0.078 2385 Dihedral : 5.473 55.378 1934 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 12.72 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1648 helix: 0.24 (0.44), residues: 145 sheet: -0.20 (0.23), residues: 501 loop : -0.39 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V1120 HIS 0.011 0.001 HIS A2315 PHE 0.019 0.001 PHE V1100 TYR 0.012 0.001 TYR A2105 ARG 0.008 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 1.77382 ( 12) link_BETA1-4 : bond 0.00371 ( 2) link_BETA1-4 : angle 2.18485 ( 6) hydrogen bonds : bond 0.02968 ( 414) hydrogen bonds : angle 5.48573 ( 1098) metal coordination : bond 0.00207 ( 3) SS BOND : bond 0.00288 ( 32) SS BOND : angle 1.31231 ( 64) covalent geometry : bond 0.00379 (13818) covalent geometry : angle 0.57825 (18739) *********************** 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 108 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: A 84 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8395 (p) REVERT: A 127 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8261 (mtpm) REVERT: A 251 LYS cc_start: 0.8808 (mptt) cc_final: 0.8543 (mptt) REVERT: A 299 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8510 (tm) REVERT: A 478 HIS cc_start: 0.8168 (m90) cc_final: 0.7429 (m170) REVERT: A 497 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7656 (p90) REVERT: A 539 MET cc_start: 0.8762 (mpt) cc_final: 0.8560 (mpp) REVERT: A 682 MET cc_start: 0.9169 (mpt) cc_final: 0.8710 (mmm) REVERT: A 2055 TYR cc_start: 0.8142 (t80) cc_final: 0.7560 (t80) REVERT: V 872 MET cc_start: 0.5756 (pmm) cc_final: 0.5481 (pmm) REVERT: V 927 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9121 (pp) REVERT: V 947 MET cc_start: 0.2988 (OUTLIER) cc_final: 0.2266 (mpm) REVERT: V 1016 GLU cc_start: 0.8585 (mp0) cc_final: 0.7994 (tm-30) REVERT: V 1076 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5970 (p0) outliers start: 34 outliers final: 17 residues processed: 97 average time/residue: 1.3612 time to fit residues: 148.2124 Evaluate side-chains 99 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 497 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 775 VAL Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 126 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 0.0000 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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** ** A1919 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 = 0.4152 r_free = 0.4152 target = 0.112990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075220 restraints weight = 29639.140| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.77 r_work: 0.3273 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13859 Z= 0.196 Angle : 0.589 11.693 18821 Z= 0.299 Chirality : 0.045 0.145 2046 Planarity : 0.004 0.041 2385 Dihedral : 5.508 55.703 1934 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.36 % Allowed : 12.79 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1648 helix: 0.26 (0.44), residues: 144 sheet: -0.24 (0.23), residues: 503 loop : -0.43 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V1120 HIS 0.011 0.001 HIS A2315 PHE 0.024 0.002 PHE A 501 TYR 0.013 0.002 TYR A2105 ARG 0.005 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 1.82631 ( 12) link_BETA1-4 : bond 0.00306 ( 2) link_BETA1-4 : angle 2.14907 ( 6) hydrogen bonds : bond 0.02989 ( 414) hydrogen bonds : angle 5.52759 ( 1098) metal coordination : bond 0.00384 ( 3) SS BOND : bond 0.00239 ( 32) SS BOND : angle 1.00930 ( 64) covalent geometry : bond 0.00448 (13818) covalent geometry : angle 0.58467 (18739) *********************** 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 113 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8586 (mmm) REVERT: A 84 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8391 (p) REVERT: A 127 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8313 (mtpm) REVERT: A 251 LYS cc_start: 0.8833 (mptt) cc_final: 0.8566 (mptt) REVERT: A 299 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8636 (tm) REVERT: A 478 HIS cc_start: 0.8180 (m90) cc_final: 0.7461 (m170) REVERT: A 497 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7652 (p90) REVERT: A 682 MET cc_start: 0.9177 (mpt) cc_final: 0.8921 (mmt) REVERT: A 2055 TYR cc_start: 0.8166 (t80) cc_final: 0.7601 (t80) REVERT: V 771 MET cc_start: 0.7627 (mmp) cc_final: 0.7366 (mmm) REVERT: V 927 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (pp) REVERT: V 947 MET cc_start: 0.3027 (OUTLIER) cc_final: 0.2247 (mpm) REVERT: V 1073 LYS cc_start: 0.9232 (mttt) cc_final: 0.8848 (pptt) REVERT: V 1076 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6117 (p0) outliers start: 35 outliers final: 20 residues processed: 101 average time/residue: 1.1445 time to fit residues: 129.9493 Evaluate side-chains 104 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 497 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1973 MET Chi-restraints excluded: chain A residue 2038 THR 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 2248 VAL 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 775 VAL Chi-restraints excluded: chain V residue 802 MET Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET Chi-restraints excluded: chain V residue 1029 SER 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 162 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 143 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.114800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076689 restraints weight = 29729.287| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.82 r_work: 0.3304 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2530 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= 0.116 Angle : 0.568 12.264 18821 Z= 0.285 Chirality : 0.044 0.153 2046 Planarity : 0.004 0.031 2385 Dihedral : 5.299 57.073 1934 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.88 % Allowed : 13.26 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1648 helix: 0.27 (0.44), residues: 145 sheet: -0.09 (0.24), residues: 491 loop : -0.36 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V1120 HIS 0.012 0.001 HIS A2315 PHE 0.020 0.001 PHE V1100 TYR 0.010 0.001 TYR A2305 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 2.15977 ( 12) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.83321 ( 6) hydrogen bonds : bond 0.02834 ( 414) hydrogen bonds : angle 5.35413 ( 1098) metal coordination : bond 0.00157 ( 3) SS BOND : bond 0.00176 ( 32) SS BOND : angle 0.85512 ( 64) covalent geometry : bond 0.00265 (13818) covalent geometry : angle 0.56361 (18739) ********************** 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 106 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: A 84 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 127 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8296 (mtpm) REVERT: A 251 LYS cc_start: 0.8788 (mptt) cc_final: 0.8520 (mptt) REVERT: A 299 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8556 (tm) REVERT: A 478 HIS cc_start: 0.8240 (m90) cc_final: 0.7498 (m170) REVERT: A 497 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7649 (p90) REVERT: A 679 PHE cc_start: 0.8271 (t80) cc_final: 0.8065 (t80) REVERT: A 682 MET cc_start: 0.9142 (mpt) cc_final: 0.8855 (mmt) REVERT: A 2055 TYR cc_start: 0.8127 (t80) cc_final: 0.7556 (t80) REVERT: V 927 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9122 (pp) REVERT: V 947 MET cc_start: 0.2999 (OUTLIER) cc_final: 0.2232 (mpm) REVERT: V 1016 GLU cc_start: 0.8597 (mp0) cc_final: 0.8007 (tm-30) REVERT: V 1076 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6144 (p0) outliers start: 28 outliers final: 14 residues processed: 99 average time/residue: 1.1305 time to fit residues: 125.6304 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 : 1.403 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 1860 THR Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 2038 THR Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2186 SER Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2304 ARG Chi-restraints excluded: chain V residue 775 VAL Chi-restraints excluded: chain V residue 927 ILE Chi-restraints excluded: chain V residue 947 MET 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 86 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.113235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075103 restraints weight = 30187.175| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.77 r_work: 0.3268 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2593 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= 0.207 Angle : 0.608 11.391 18821 Z= 0.305 Chirality : 0.045 0.141 2046 Planarity : 0.004 0.035 2385 Dihedral : 5.452 57.114 1934 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.95 % Allowed : 13.73 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1648 helix: 0.25 (0.44), residues: 144 sheet: -0.22 (0.23), residues: 503 loop : -0.41 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V1120 HIS 0.010 0.001 HIS A2315 PHE 0.024 0.002 PHE A 501 TYR 0.014 0.002 TYR A2105 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 4) link_NAG-ASN : angle 2.17503 ( 12) link_BETA1-4 : bond 0.00294 ( 2) link_BETA1-4 : angle 2.10414 ( 6) hydrogen bonds : bond 0.03067 ( 414) hydrogen bonds : angle 5.47895 ( 1098) metal coordination : bond 0.00352 ( 3) SS BOND : bond 0.00232 ( 32) SS BOND : angle 0.92219 ( 64) covalent geometry : bond 0.00474 (13818) covalent geometry : angle 0.60283 (18739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14009.40 seconds wall clock time: 245 minutes 21.70 seconds (14721.70 seconds total)