Starting phenix.real_space_refine on Thu Feb 5 05:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.map" model { file = "/net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uaj_63984/02_2026/9uaj_63984.cif" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 9532 2.51 5 N 2442 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15208 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1464 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 174} Chain: "B" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1419 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 170} Chain: "C" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1439 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 169} Chain: "E" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1489 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 174} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1464 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 174} Chain: "G" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1489 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 174} Chain: "H" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1407 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 168} Chain: "I" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1439 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170} Chain: "J" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1419 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 170} Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'08O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'08O': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'08O': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'08O': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 15208 At special positions: 0 Unit cell: (92.22, 92.22, 111.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 3180 8.00 N 2442 7.00 C 9532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG K 1 " - " FUC K 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG P 1 " - " FUC P 2 " " NAG R 1 " - " FUC R 2 " BETA1-4 " NAG K 1 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 3 " " NAG P 1 " - " NAG P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG D 301 " - " ASN D 46 " " NAG H 301 " - " ASN H 46 " " NAG K 1 " - " ASN A 113 " " NAG L 1 " - " ASN B 109 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 199 " " NAG O 1 " - " ASN E 119 " " NAG P 1 " - " ASN F 113 " " NAG Q 1 " - " ASN G 199 " " NAG R 1 " - " ASN G 119 " " NAG S 1 " - " ASN H 111 " " NAG T 1 " - " ASN J 109 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 448.1 milliseconds 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3418 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 11 sheets defined 33.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 127 through 149 removed outlier: 4.843A pdb=" N HIS A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 removed outlier: 4.009A pdb=" N ARG A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.625A pdb=" N SER B 144 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'C' and resid 37 through 44 removed outlier: 4.513A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 125 through 144 removed outlier: 4.281A pdb=" N GLY C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU C 143 " --> pdb=" O HIS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 90 through 97 Processing helix chain 'D' and resid 125 through 144 removed outlier: 3.774A pdb=" N THR D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.998A pdb=" N ARG D 174 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 133 through 152 removed outlier: 4.554A pdb=" N ASP E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 187 through 193 removed outlier: 6.108A pdb=" N ASN E 190 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 70 through 76 Processing helix chain 'F' and resid 92 through 99 Processing helix chain 'F' and resid 127 through 147 removed outlier: 4.741A pdb=" N HIS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 183 removed outlier: 4.633A pdb=" N ARG F 178 " --> pdb=" O CYS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'G' and resid 41 through 48 Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 133 through 152 removed outlier: 4.575A pdb=" N ASP G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 180 through 186 removed outlier: 3.702A pdb=" N CYS G 186 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 193 removed outlier: 6.156A pdb=" N ASN G 190 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'H' and resid 40 through 46 Processing helix chain 'H' and resid 70 through 74 Processing helix chain 'H' and resid 90 through 97 Processing helix chain 'H' and resid 125 through 144 removed outlier: 4.098A pdb=" N THR H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 143 " --> pdb=" O TYR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 184 removed outlier: 4.237A pdb=" N ARG H 174 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR H 177 " --> pdb=" O ARG H 174 " (cutoff:3.500A) Proline residue: H 178 - end of helix Processing helix chain 'H' and resid 185 through 187 No H-bonds generated for 'chain 'H' and resid 185 through 187' Processing helix chain 'I' and resid 37 through 43 Processing helix chain 'I' and resid 67 through 74 Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 91 through 98 Processing helix chain 'I' and resid 125 through 144 removed outlier: 4.234A pdb=" N GLY I 142 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU I 143 " --> pdb=" O HIS I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 178 Processing helix chain 'J' and resid 33 through 41 Processing helix chain 'J' and resid 65 through 73 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'J' and resid 170 through 177 Processing helix chain 'J' and resid 178 through 183 removed outlier: 3.595A pdb=" N PHE J 182 " --> pdb=" O ILE J 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 4.963A pdb=" N ARG A 60 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS A 66 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL A 49 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 114 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS A 163 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 83 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 29 removed outlier: 6.159A pdb=" N LYS B 63 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 46 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 110 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS B 159 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 146 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 7.687A pdb=" N GLY B 54 " --> pdb=" O VAL C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 29 removed outlier: 6.341A pdb=" N ARG C 65 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 48 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 112 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ARG C 161 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 26 through 32 removed outlier: 5.133A pdb=" N LYS D 63 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 55 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU D 81 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP D 32 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 26 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 29 through 36 removed outlier: 5.225A pdb=" N SER E 65 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 205 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU E 120 " --> pdb=" O ILE E 205 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS E 169 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 23 through 30 removed outlier: 4.961A pdb=" N ARG F 60 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS F 51 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS F 66 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL F 49 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU F 114 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS F 163 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 29 through 36 removed outlier: 5.465A pdb=" N SER G 65 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU G 71 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE G 54 " --> pdb=" O GLU G 71 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU G 120 " --> pdb=" O ILE G 205 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LYS G 169 " --> pdb=" O THR G 162 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN G 156 " --> pdb=" O ASN G 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 32 removed outlier: 5.038A pdb=" N LYS H 63 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR H 55 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU H 81 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP H 32 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU H 26 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 22 through 29 removed outlier: 6.279A pdb=" N ARG I 65 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL I 48 " --> pdb=" O ARG I 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL I 112 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG I 161 " --> pdb=" O ALA I 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 24 through 30 removed outlier: 5.163A pdb=" N ARG J 57 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS J 63 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE J 46 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS J 49 " --> pdb=" O LEU J 198 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL J 110 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS J 159 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR J 146 " --> pdb=" O ASN J 165 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3876 1.33 - 1.45: 2594 1.45 - 1.57: 8619 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 15185 Sorted by residual: bond pdb=" N ILE F 87 " pdb=" CA ILE F 87 " ideal model delta sigma weight residual 1.456 1.490 -0.034 8.70e-03 1.32e+04 1.52e+01 bond pdb=" N VAL I 197 " pdb=" CA VAL I 197 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" C LYS I 193 " pdb=" N PRO I 194 " ideal model delta sigma weight residual 1.332 1.372 -0.040 1.32e-02 5.74e+03 9.32e+00 bond pdb=" N ILE G 89 " pdb=" CA ILE G 89 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.96e+00 bond pdb=" N VAL F 35 " pdb=" CA VAL F 35 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 ... (remaining 15180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 20125 2.33 - 4.67: 372 4.67 - 7.00: 20 7.00 - 9.33: 10 9.33 - 11.67: 12 Bond angle restraints: 20539 Sorted by residual: angle pdb=" N TYR J 147 " pdb=" CA TYR J 147 " pdb=" CB TYR J 147 " ideal model delta sigma weight residual 111.24 104.81 6.43 1.58e+00 4.01e-01 1.66e+01 angle pdb=" N ARG C 37 " pdb=" CA ARG C 37 " pdb=" C ARG C 37 " ideal model delta sigma weight residual 113.28 108.32 4.96 1.22e+00 6.72e-01 1.65e+01 angle pdb=" C16 08O F 301 " pdb=" C17 08O F 301 " pdb=" C18 08O F 301 " ideal model delta sigma weight residual 114.91 103.24 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C16 08O A 301 " pdb=" C17 08O A 301 " pdb=" C18 08O A 301 " ideal model delta sigma weight residual 114.91 103.79 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C16 08O B 201 " pdb=" C17 08O B 201 " pdb=" C18 08O B 201 " ideal model delta sigma weight residual 114.91 103.97 10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 20534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 9084 29.55 - 59.11: 455 59.11 - 88.66: 43 88.66 - 118.21: 2 118.21 - 147.76: 2 Dihedral angle restraints: 9586 sinusoidal: 4289 harmonic: 5297 Sorted by residual: dihedral pdb=" CA PHE F 172 " pdb=" C PHE F 172 " pdb=" N ARG F 173 " pdb=" CA ARG F 173 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE D 165 " pdb=" C PHE D 165 " pdb=" N LEU D 166 " pdb=" CA LEU D 166 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N PRO A 171 " pdb=" CA PRO A 171 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1918 0.061 - 0.122: 416 0.122 - 0.183: 45 0.183 - 0.244: 6 0.244 - 0.305: 2 Chirality restraints: 2387 Sorted by residual: chirality pdb=" C2 NAG P 1 " pdb=" C1 NAG P 1 " pdb=" C3 NAG P 1 " pdb=" N2 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE E 163 " pdb=" CA ILE E 163 " pdb=" CG1 ILE E 163 " pdb=" CG2 ILE E 163 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LEU F 109 " pdb=" N LEU F 109 " pdb=" C LEU F 109 " pdb=" CB LEU F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2384 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 174 " -0.280 9.50e-02 1.11e+02 1.26e-01 9.69e+00 pdb=" NE ARG D 174 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 174 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 174 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 174 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 120 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C LYS H 120 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS H 120 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU H 121 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 176 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO G 177 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " 0.025 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2941 2.77 - 3.31: 13422 3.31 - 3.84: 26444 3.84 - 4.37: 33167 4.37 - 4.90: 54876 Nonbonded interactions: 130850 Sorted by model distance: nonbonded pdb=" O HOH G 303 " pdb=" O HOH G 305 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR B 196 " pdb=" OD1 ASP C 75 " model vdw 2.260 3.040 nonbonded pdb=" O GLY H 123 " pdb=" O HOH H 401 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR F 40 " pdb=" O PRO F 81 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP F 182 " pdb=" OH TYR J 156 " model vdw 2.283 3.040 ... (remaining 130845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 24 through 202 or resid 301)) selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.540 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 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 : 0.007 0.069 15211 Z= 0.355 Angle : 0.781 11.668 20617 Z= 0.437 Chirality : 0.052 0.305 2387 Planarity : 0.005 0.126 2597 Dihedral : 16.325 147.764 6168 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.19 % Allowed : 17.67 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1797 helix: 0.77 (0.23), residues: 520 sheet: 0.99 (0.21), residues: 599 loop : 0.22 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 97 TYR 0.013 0.002 TYR F 85 PHE 0.020 0.002 PHE H 158 TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00690 (15185) covalent geometry : angle 0.77173 (20539) hydrogen bonds : bond 0.11278 ( 725) hydrogen bonds : angle 5.36779 ( 1995) link_BETA1-3 : bond 0.00791 ( 4) link_BETA1-3 : angle 2.24179 ( 12) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.62647 ( 30) link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.43723 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 0.636 Fit side-chains REVERT: A 68 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8182 (mtp85) REVERT: C 67 ASP cc_start: 0.8555 (p0) cc_final: 0.8277 (p0) REVERT: C 69 GLN cc_start: 0.8235 (mp10) cc_final: 0.7953 (mp10) REVERT: C 148 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8204 (mtm110) REVERT: E 88 LYS cc_start: 0.8670 (mmtp) cc_final: 0.7881 (mppt) REVERT: F 38 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7904 (mp0) REVERT: G 114 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8303 (mtp-110) REVERT: G 150 ASP cc_start: 0.8918 (m-30) cc_final: 0.8613 (m-30) REVERT: I 32 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8100 (mptt) REVERT: I 59 ARG cc_start: 0.8534 (ttm110) cc_final: 0.7919 (ttt180) REVERT: I 189 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8315 (mm-30) REVERT: J 21 ASN cc_start: 0.8802 (m-40) cc_final: 0.8049 (p0) outliers start: 3 outliers final: 1 residues processed: 263 average time/residue: 0.7793 time to fit residues: 219.8954 Evaluate side-chains 248 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN H 79 HIS H 141 ASN I 47 GLN I 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.068236 restraints weight = 21830.593| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.38 r_work: 0.2712 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15211 Z= 0.175 Angle : 0.564 9.689 20617 Z= 0.292 Chirality : 0.046 0.286 2387 Planarity : 0.004 0.046 2597 Dihedral : 8.242 150.401 2584 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.23 % Allowed : 16.86 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1797 helix: 1.24 (0.24), residues: 504 sheet: 1.07 (0.21), residues: 595 loop : 0.31 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 59 TYR 0.013 0.001 TYR D 139 PHE 0.015 0.001 PHE H 158 TRP 0.007 0.001 TRP G 108 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00406 (15185) covalent geometry : angle 0.55076 (20539) hydrogen bonds : bond 0.04149 ( 725) hydrogen bonds : angle 4.80964 ( 1995) link_BETA1-3 : bond 0.00800 ( 4) link_BETA1-3 : angle 2.17707 ( 12) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 1.48817 ( 30) link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 2.42344 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 0.450 Fit side-chains REVERT: B 70 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8492 (tm130) REVERT: C 59 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8369 (mmm-85) REVERT: C 69 GLN cc_start: 0.8285 (mp10) cc_final: 0.7953 (mp10) REVERT: C 148 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8135 (mtm110) REVERT: E 88 LYS cc_start: 0.8601 (mmtp) cc_final: 0.7774 (mppt) REVERT: F 38 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7898 (mp0) REVERT: F 175 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7762 (ttt180) REVERT: G 114 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8331 (mtp-110) REVERT: G 150 ASP cc_start: 0.8932 (m-30) cc_final: 0.8615 (m-30) REVERT: I 32 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8072 (mptt) REVERT: I 59 ARG cc_start: 0.8525 (ttm110) cc_final: 0.7820 (ttt180) REVERT: I 125 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9001 (p) REVERT: J 21 ASN cc_start: 0.8807 (m-40) cc_final: 0.8039 (p0) outliers start: 36 outliers final: 16 residues processed: 267 average time/residue: 0.7792 time to fit residues: 223.4773 Evaluate side-chains 262 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 111 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN H 79 HIS I 47 GLN I 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069409 restraints weight = 21985.855| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.39 r_work: 0.2737 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15211 Z= 0.129 Angle : 0.523 9.652 20617 Z= 0.270 Chirality : 0.044 0.275 2387 Planarity : 0.004 0.046 2597 Dihedral : 7.847 146.182 2582 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.48 % Allowed : 17.23 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1797 helix: 1.40 (0.24), residues: 506 sheet: 1.17 (0.21), residues: 593 loop : 0.36 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 148 TYR 0.011 0.001 TYR D 139 PHE 0.013 0.001 PHE D 158 TRP 0.009 0.001 TRP D 31 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00295 (15185) covalent geometry : angle 0.51011 (20539) hydrogen bonds : bond 0.03418 ( 725) hydrogen bonds : angle 4.62972 ( 1995) link_BETA1-3 : bond 0.00885 ( 4) link_BETA1-3 : angle 2.12333 ( 12) link_BETA1-4 : bond 0.00450 ( 10) link_BETA1-4 : angle 1.40510 ( 30) link_NAG-ASN : bond 0.00183 ( 12) link_NAG-ASN : angle 2.29297 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.650 Fit side-chains REVERT: A 87 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 80 ARG cc_start: 0.7747 (tmt-80) cc_final: 0.7439 (tmt-80) REVERT: C 59 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.8313 (mmm-85) REVERT: C 69 GLN cc_start: 0.8302 (mp10) cc_final: 0.7970 (mp10) REVERT: C 148 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8126 (mtm110) REVERT: D 117 MET cc_start: 0.9009 (ttp) cc_final: 0.8782 (ttm) REVERT: E 88 LYS cc_start: 0.8600 (mmtp) cc_final: 0.7770 (mppt) REVERT: F 38 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7836 (mp0) REVERT: F 175 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7800 (mtt180) REVERT: G 114 ARG cc_start: 0.8671 (mtm110) cc_final: 0.8340 (mtp-110) REVERT: G 150 ASP cc_start: 0.8918 (m-30) cc_final: 0.8611 (m-30) REVERT: I 32 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8093 (mptt) REVERT: I 59 ARG cc_start: 0.8509 (ttm110) cc_final: 0.7807 (ttt180) REVERT: I 125 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9024 (p) REVERT: J 21 ASN cc_start: 0.8784 (m-40) cc_final: 0.8019 (p0) REVERT: J 95 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8325 (m-30) outliers start: 40 outliers final: 18 residues processed: 274 average time/residue: 0.7405 time to fit residues: 218.3631 Evaluate side-chains 267 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS H 141 ASN I 47 GLN I 147 HIS I 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067639 restraints weight = 22028.452| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.38 r_work: 0.2700 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15211 Z= 0.223 Angle : 0.578 9.719 20617 Z= 0.299 Chirality : 0.047 0.300 2387 Planarity : 0.004 0.046 2597 Dihedral : 7.823 133.393 2582 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.85 % Allowed : 16.74 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1797 helix: 1.33 (0.24), residues: 506 sheet: 1.09 (0.21), residues: 595 loop : 0.32 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 37 TYR 0.012 0.002 TYR D 139 PHE 0.018 0.002 PHE H 158 TRP 0.007 0.001 TRP J 128 HIS 0.004 0.001 HIS I 162 Details of bonding type rmsd covalent geometry : bond 0.00533 (15185) covalent geometry : angle 0.56636 (20539) hydrogen bonds : bond 0.03970 ( 725) hydrogen bonds : angle 4.72307 ( 1995) link_BETA1-3 : bond 0.00855 ( 4) link_BETA1-3 : angle 2.10322 ( 12) link_BETA1-4 : bond 0.00449 ( 10) link_BETA1-4 : angle 1.46225 ( 30) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.30412 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: B 80 ARG cc_start: 0.7728 (tmt-80) cc_final: 0.7260 (tmt-80) REVERT: C 69 GLN cc_start: 0.8292 (mp10) cc_final: 0.7948 (mp10) REVERT: C 73 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8618 (ttpt) REVERT: C 148 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8115 (mtm110) REVERT: C 178 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8426 (ptp-110) REVERT: E 88 LYS cc_start: 0.8605 (mmtp) cc_final: 0.7736 (mppt) REVERT: F 38 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7856 (mp0) REVERT: F 175 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7824 (mtt180) REVERT: G 114 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8349 (mtp-110) REVERT: G 150 ASP cc_start: 0.8931 (m-30) cc_final: 0.8614 (m-30) REVERT: H 81 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8659 (tp) REVERT: I 32 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8108 (mptt) REVERT: I 59 ARG cc_start: 0.8542 (ttm110) cc_final: 0.7840 (ttt180) REVERT: J 21 ASN cc_start: 0.8812 (m-40) cc_final: 0.8003 (p0) outliers start: 46 outliers final: 26 residues processed: 276 average time/residue: 0.7524 time to fit residues: 223.3186 Evaluate side-chains 273 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 49 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS I 47 GLN I 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.067332 restraints weight = 21960.234| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.40 r_work: 0.2691 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15211 Z= 0.231 Angle : 0.589 9.736 20617 Z= 0.305 Chirality : 0.047 0.303 2387 Planarity : 0.005 0.052 2597 Dihedral : 7.785 123.064 2582 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.04 % Allowed : 16.86 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1797 helix: 1.28 (0.24), residues: 508 sheet: 1.11 (0.21), residues: 595 loop : 0.28 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 42 TYR 0.013 0.002 TYR D 139 PHE 0.019 0.002 PHE H 158 TRP 0.008 0.001 TRP H 31 HIS 0.004 0.001 HIS I 162 Details of bonding type rmsd covalent geometry : bond 0.00549 (15185) covalent geometry : angle 0.57746 (20539) hydrogen bonds : bond 0.04021 ( 725) hydrogen bonds : angle 4.74043 ( 1995) link_BETA1-3 : bond 0.00850 ( 4) link_BETA1-3 : angle 2.07655 ( 12) link_BETA1-4 : bond 0.00442 ( 10) link_BETA1-4 : angle 1.46535 ( 30) link_NAG-ASN : bond 0.00303 ( 12) link_NAG-ASN : angle 2.30565 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8119 (pt) REVERT: B 80 ARG cc_start: 0.7671 (tmt-80) cc_final: 0.7390 (tmt-80) REVERT: C 69 GLN cc_start: 0.8287 (mp10) cc_final: 0.7933 (mp10) REVERT: C 73 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (ttpt) REVERT: C 148 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8115 (mtm110) REVERT: C 174 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: C 178 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8487 (ptp-170) REVERT: E 88 LYS cc_start: 0.8603 (mmtp) cc_final: 0.7737 (mppt) REVERT: F 38 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7847 (mp0) REVERT: F 175 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7711 (ttt180) REVERT: G 114 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8348 (mtp-110) REVERT: G 150 ASP cc_start: 0.8947 (m-30) cc_final: 0.8630 (m-30) REVERT: H 81 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8670 (tp) REVERT: I 32 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8091 (mptt) REVERT: I 59 ARG cc_start: 0.8539 (ttm110) cc_final: 0.7835 (ttt180) REVERT: J 21 ASN cc_start: 0.8807 (m-40) cc_final: 0.7999 (p0) REVERT: J 95 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7958 (m-30) outliers start: 49 outliers final: 29 residues processed: 270 average time/residue: 0.7471 time to fit residues: 216.9155 Evaluate side-chains 279 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 111 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS H 141 ASN I 47 GLN I 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.068727 restraints weight = 21752.409| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.36 r_work: 0.2726 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15211 Z= 0.138 Angle : 0.537 9.663 20617 Z= 0.278 Chirality : 0.044 0.280 2387 Planarity : 0.004 0.047 2597 Dihedral : 7.481 113.114 2582 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.73 % Allowed : 17.54 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1797 helix: 1.42 (0.24), residues: 508 sheet: 1.19 (0.21), residues: 591 loop : 0.31 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 42 TYR 0.011 0.001 TYR C 151 PHE 0.014 0.001 PHE D 158 TRP 0.010 0.001 TRP H 31 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00321 (15185) covalent geometry : angle 0.52503 (20539) hydrogen bonds : bond 0.03380 ( 725) hydrogen bonds : angle 4.59321 ( 1995) link_BETA1-3 : bond 0.00848 ( 4) link_BETA1-3 : angle 2.05120 ( 12) link_BETA1-4 : bond 0.00475 ( 10) link_BETA1-4 : angle 1.38760 ( 30) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 2.21447 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8106 (pt) REVERT: B 80 ARG cc_start: 0.7674 (tmt-80) cc_final: 0.7387 (tmt-80) REVERT: C 69 GLN cc_start: 0.8292 (mp10) cc_final: 0.7951 (mp10) REVERT: C 73 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8666 (ttpt) REVERT: C 148 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8113 (mtm110) REVERT: C 174 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: D 33 LYS cc_start: 0.8000 (mmpt) cc_final: 0.7776 (mtpt) REVERT: E 88 LYS cc_start: 0.8607 (mmtp) cc_final: 0.7748 (mppt) REVERT: F 38 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7853 (mp0) REVERT: F 175 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7710 (ttt180) REVERT: G 114 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8373 (mtp-110) REVERT: G 150 ASP cc_start: 0.8940 (m-30) cc_final: 0.8631 (m-30) REVERT: H 192 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8347 (mt-10) REVERT: I 32 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8096 (mptt) REVERT: I 59 ARG cc_start: 0.8526 (ttm110) cc_final: 0.7844 (ttt180) REVERT: I 125 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9014 (p) REVERT: J 21 ASN cc_start: 0.8787 (m-40) cc_final: 0.8011 (p0) REVERT: J 95 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.7937 (m-30) outliers start: 44 outliers final: 25 residues processed: 275 average time/residue: 0.7347 time to fit residues: 217.3706 Evaluate side-chains 275 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS I 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.068540 restraints weight = 21770.313| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.36 r_work: 0.2718 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15211 Z= 0.167 Angle : 0.555 9.688 20617 Z= 0.287 Chirality : 0.045 0.288 2387 Planarity : 0.004 0.056 2597 Dihedral : 7.429 108.981 2582 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.54 % Allowed : 17.67 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1797 helix: 1.43 (0.24), residues: 508 sheet: 1.19 (0.21), residues: 591 loop : 0.31 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 42 TYR 0.010 0.001 TYR C 151 PHE 0.015 0.001 PHE D 158 TRP 0.008 0.001 TRP H 31 HIS 0.005 0.001 HIS I 162 Details of bonding type rmsd covalent geometry : bond 0.00394 (15185) covalent geometry : angle 0.54360 (20539) hydrogen bonds : bond 0.03533 ( 725) hydrogen bonds : angle 4.60611 ( 1995) link_BETA1-3 : bond 0.00825 ( 4) link_BETA1-3 : angle 2.03163 ( 12) link_BETA1-4 : bond 0.00453 ( 10) link_BETA1-4 : angle 1.39209 ( 30) link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 2.18848 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8106 (pt) REVERT: B 80 ARG cc_start: 0.7667 (tmt-80) cc_final: 0.7375 (tmt-80) REVERT: C 69 GLN cc_start: 0.8286 (mp10) cc_final: 0.7941 (mp10) REVERT: C 73 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8680 (ttpt) REVERT: C 148 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8107 (mtm110) REVERT: C 174 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: D 33 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7786 (mtpt) REVERT: E 88 LYS cc_start: 0.8608 (mmtp) cc_final: 0.7747 (mppt) REVERT: F 38 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7857 (mp0) REVERT: F 175 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7713 (ttt180) REVERT: G 114 ARG cc_start: 0.8687 (mtm110) cc_final: 0.8379 (mtp-110) REVERT: G 150 ASP cc_start: 0.8937 (m-30) cc_final: 0.8624 (m-30) REVERT: I 32 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8111 (mptt) REVERT: I 59 ARG cc_start: 0.8529 (ttm110) cc_final: 0.7843 (ttt180) REVERT: J 21 ASN cc_start: 0.8775 (m-40) cc_final: 0.7991 (p0) REVERT: J 95 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.7933 (m-30) outliers start: 41 outliers final: 29 residues processed: 271 average time/residue: 0.7844 time to fit residues: 228.1559 Evaluate side-chains 275 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS H 141 ASN I 47 GLN I 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.067148 restraints weight = 22051.751| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.37 r_work: 0.2692 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15211 Z= 0.250 Angle : 0.610 9.742 20617 Z= 0.315 Chirality : 0.048 0.309 2387 Planarity : 0.005 0.059 2597 Dihedral : 7.622 111.221 2582 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.60 % Allowed : 17.79 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1797 helix: 1.30 (0.24), residues: 508 sheet: 1.12 (0.21), residues: 595 loop : 0.29 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 42 TYR 0.013 0.002 TYR D 139 PHE 0.020 0.002 PHE H 158 TRP 0.008 0.001 TRP J 128 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00596 (15185) covalent geometry : angle 0.59892 (20539) hydrogen bonds : bond 0.04083 ( 725) hydrogen bonds : angle 4.73885 ( 1995) link_BETA1-3 : bond 0.00916 ( 4) link_BETA1-3 : angle 2.01792 ( 12) link_BETA1-4 : bond 0.00424 ( 10) link_BETA1-4 : angle 1.45317 ( 30) link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.28255 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8098 (pt) REVERT: B 80 ARG cc_start: 0.7653 (tmt-80) cc_final: 0.7362 (tmt-80) REVERT: C 67 ASP cc_start: 0.8627 (p0) cc_final: 0.8249 (p0) REVERT: C 69 GLN cc_start: 0.8279 (mp10) cc_final: 0.7894 (mp10) REVERT: C 73 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (ttpt) REVERT: C 148 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8105 (mtm110) REVERT: C 174 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: E 88 LYS cc_start: 0.8605 (mmtp) cc_final: 0.7756 (mppt) REVERT: F 38 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7840 (mp0) REVERT: F 175 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7742 (ttt180) REVERT: G 150 ASP cc_start: 0.8943 (m-30) cc_final: 0.8630 (m-30) REVERT: I 32 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8098 (mptt) REVERT: I 59 ARG cc_start: 0.8546 (ttm110) cc_final: 0.7854 (ttt180) REVERT: J 21 ASN cc_start: 0.8792 (m-40) cc_final: 0.7993 (p0) REVERT: J 95 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7948 (m-30) outliers start: 42 outliers final: 30 residues processed: 265 average time/residue: 0.7753 time to fit residues: 221.3052 Evaluate side-chains 274 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 199 ARG Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 168 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 169 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS I 47 GLN ** I 167 ASN ** 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 = 0.3259 r_free = 0.3259 target = 0.091236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.070408 restraints weight = 21935.068| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.38 r_work: 0.2763 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15211 Z= 0.103 Angle : 0.519 9.622 20617 Z= 0.268 Chirality : 0.044 0.264 2387 Planarity : 0.004 0.055 2597 Dihedral : 6.973 99.593 2582 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.92 % Allowed : 18.60 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1797 helix: 1.53 (0.24), residues: 506 sheet: 1.29 (0.21), residues: 588 loop : 0.34 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 42 TYR 0.009 0.001 TYR C 151 PHE 0.010 0.001 PHE D 158 TRP 0.014 0.001 TRP D 31 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00235 (15185) covalent geometry : angle 0.50759 (20539) hydrogen bonds : bond 0.02889 ( 725) hydrogen bonds : angle 4.46903 ( 1995) link_BETA1-3 : bond 0.00845 ( 4) link_BETA1-3 : angle 1.96547 ( 12) link_BETA1-4 : bond 0.00507 ( 10) link_BETA1-4 : angle 1.29482 ( 30) link_NAG-ASN : bond 0.00132 ( 12) link_NAG-ASN : angle 2.12657 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.518 Fit side-chains REVERT: A 87 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8093 (pt) REVERT: A 146 MET cc_start: 0.7800 (tmm) cc_final: 0.7413 (tmt) REVERT: B 70 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8394 (tm130) REVERT: B 80 ARG cc_start: 0.7664 (tmt-80) cc_final: 0.7374 (tmt-80) REVERT: C 69 GLN cc_start: 0.8296 (mp10) cc_final: 0.7953 (mp10) REVERT: C 148 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8119 (mtm110) REVERT: C 174 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: D 117 MET cc_start: 0.8999 (ttp) cc_final: 0.8779 (ttm) REVERT: E 88 LYS cc_start: 0.8586 (mmtp) cc_final: 0.7735 (mppt) REVERT: F 38 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7868 (mp0) REVERT: F 146 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7879 (tmt) REVERT: F 175 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7721 (ttt180) REVERT: G 114 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8302 (mtm-85) REVERT: G 150 ASP cc_start: 0.8921 (m-30) cc_final: 0.8600 (m-30) REVERT: G 154 GLN cc_start: 0.8931 (mt0) cc_final: 0.8722 (pt0) REVERT: I 32 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8105 (mptt) REVERT: I 59 ARG cc_start: 0.8519 (ttm110) cc_final: 0.7828 (ttt180) REVERT: I 125 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9027 (p) REVERT: J 95 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7991 (m-30) outliers start: 31 outliers final: 15 residues processed: 276 average time/residue: 0.7919 time to fit residues: 234.6412 Evaluate side-chains 271 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 151 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN G 27 GLN H 79 HIS H 141 ASN I 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.069335 restraints weight = 22081.084| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.37 r_work: 0.2747 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15211 Z= 0.134 Angle : 0.534 9.657 20617 Z= 0.277 Chirality : 0.044 0.279 2387 Planarity : 0.004 0.063 2597 Dihedral : 6.907 97.452 2582 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.74 % Allowed : 18.91 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1797 helix: 1.58 (0.24), residues: 506 sheet: 1.30 (0.21), residues: 588 loop : 0.36 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 42 TYR 0.010 0.001 TYR I 151 PHE 0.013 0.001 PHE D 158 TRP 0.009 0.001 TRP D 31 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00313 (15185) covalent geometry : angle 0.52329 (20539) hydrogen bonds : bond 0.03169 ( 725) hydrogen bonds : angle 4.48598 ( 1995) link_BETA1-3 : bond 0.00822 ( 4) link_BETA1-3 : angle 1.97031 ( 12) link_BETA1-4 : bond 0.00469 ( 10) link_BETA1-4 : angle 1.31423 ( 30) link_NAG-ASN : bond 0.00155 ( 12) link_NAG-ASN : angle 2.10590 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.559 Fit side-chains REVERT: A 87 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8094 (pt) REVERT: B 70 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8349 (tm130) REVERT: B 80 ARG cc_start: 0.7679 (tmt-80) cc_final: 0.7391 (tmt-80) REVERT: C 69 GLN cc_start: 0.8275 (mp10) cc_final: 0.7949 (mp10) REVERT: C 148 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8120 (mtm110) REVERT: C 174 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: D 117 MET cc_start: 0.9014 (ttp) cc_final: 0.8791 (ttm) REVERT: E 88 LYS cc_start: 0.8582 (mmtp) cc_final: 0.7732 (mppt) REVERT: F 38 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7872 (mp0) REVERT: F 146 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7912 (tmt) REVERT: F 175 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7676 (ttt180) REVERT: G 114 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8349 (mtm-85) REVERT: G 150 ASP cc_start: 0.8915 (m-30) cc_final: 0.8595 (m-30) REVERT: G 154 GLN cc_start: 0.8915 (mt0) cc_final: 0.8712 (pt0) REVERT: I 32 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8112 (mptt) REVERT: I 59 ARG cc_start: 0.8530 (ttm110) cc_final: 0.7843 (ttt180) REVERT: I 125 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9035 (p) REVERT: J 95 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8015 (m-30) outliers start: 28 outliers final: 15 residues processed: 265 average time/residue: 0.7793 time to fit residues: 221.5857 Evaluate side-chains 268 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 175 ARG Chi-restraints excluded: chain G residue 108 TRP Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 39 SER Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 0.9980 chunk 167 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS I 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.071616 restraints weight = 21656.353| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.36 r_work: 0.2784 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15211 Z= 0.104 Angle : 0.516 9.588 20617 Z= 0.266 Chirality : 0.043 0.266 2387 Planarity : 0.004 0.058 2597 Dihedral : 6.533 88.352 2582 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.43 % Allowed : 19.34 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1797 helix: 1.65 (0.24), residues: 506 sheet: 1.34 (0.22), residues: 588 loop : 0.43 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 42 TYR 0.008 0.001 TYR C 151 PHE 0.009 0.001 PHE F 165 TRP 0.012 0.001 TRP D 31 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00238 (15185) covalent geometry : angle 0.50570 (20539) hydrogen bonds : bond 0.02784 ( 725) hydrogen bonds : angle 4.37744 ( 1995) link_BETA1-3 : bond 0.00769 ( 4) link_BETA1-3 : angle 1.91838 ( 12) link_BETA1-4 : bond 0.00485 ( 10) link_BETA1-4 : angle 1.22815 ( 30) link_NAG-ASN : bond 0.00129 ( 12) link_NAG-ASN : angle 2.03085 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6278.74 seconds wall clock time: 107 minutes 30.11 seconds (6450.11 seconds total)