Starting phenix.real_space_refine on Thu Feb 5 21:59:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltu_63381/02_2026/9ltu_63381.map" } resolution = 2.44 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= 0.001 sd= 0.066 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Mg 24 5.21 5 S 70 5.16 5 C 14059 2.51 5 N 2932 2.21 5 O 3217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 20306 Number of models: 1 Model: "" Number of chains: 47 Chain: "0" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "8" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2785 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 27, 'TRANS': 329} Chain: "H" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2015 Classifications: {'peptide': 255} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 236} Chain: "L" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain: "M" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2634 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 310} Chain: "a" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "b" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "c" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "d" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "f" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "g" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "h" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "j" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "k" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "l" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "m" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "n" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "p" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "0" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 300 Unusual residues: {'BCL': 2, 'BPH': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 304 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 195 Unusual residues: {'BCL': 1, 'SPN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.58, per 1000 atoms: 0.23 Number of scatterers: 20306 At special positions: 0 Unit cell: (143.56, 119.31, 150.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 70 16.00 Mg 24 11.99 O 3217 8.00 N 2932 7.00 C 14059 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=27, symmetry=0 Number of additional bonds: simple=27, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 755.9 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 8 sheets defined 66.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain '0' and resid 12 through 45 removed outlier: 3.737A pdb=" N ALA 0 16 " --> pdb=" O THR 0 12 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 11 Processing helix chain '7' and resid 12 through 37 removed outlier: 4.437A pdb=" N VAL 7 16 " --> pdb=" O ASP 7 12 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY 7 21 " --> pdb=" O PHE 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 44 through 50 Processing helix chain '8' and resid 13 through 34 removed outlier: 4.121A pdb=" N VAL 8 22 " --> pdb=" O GLU 8 18 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER 8 25 " --> pdb=" O SER 8 21 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TRP 8 28 " --> pdb=" O MET 8 24 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU 8 29 " --> pdb=" O SER 8 25 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL 8 33 " --> pdb=" O LEU 8 29 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 39 removed outlier: 4.082A pdb=" N HIS 8 38 " --> pdb=" O ALA 8 34 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 10 Processing helix chain '9' and resid 12 through 38 removed outlier: 3.655A pdb=" N VAL 9 16 " --> pdb=" O ASP 9 12 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 9 17 " --> pdb=" O PRO 9 13 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL 9 18 " --> pdb=" O ARG 9 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 9 22 " --> pdb=" O VAL 9 18 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET 9 30 " --> pdb=" O LEU 9 26 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 51 Processing helix chain 'C' and resid 18 through 28 Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.945A pdb=" N GLY C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.521A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.898A pdb=" N VAL C 199 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.838A pdb=" N HIS C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 removed outlier: 4.241A pdb=" N THR C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.666A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 333 removed outlier: 4.195A pdb=" N CYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 352 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'H' and resid 10 through 34 removed outlier: 3.578A pdb=" N ASN H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 185 through 188 removed outlier: 3.639A pdb=" N GLY H 188 " --> pdb=" O PRO H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 188' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 212 through 219 removed outlier: 3.545A pdb=" N PHE H 216 " --> pdb=" O GLY H 213 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS H 217 " --> pdb=" O LYS H 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN H 218 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL H 219 " --> pdb=" O PHE H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 247 removed outlier: 3.755A pdb=" N GLY H 243 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.503A pdb=" N GLN L 88 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.753A pdb=" N VAL L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.038A pdb=" N ASP L 156 " --> pdb=" O TRP L 152 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL L 158 " --> pdb=" O HIS L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 Processing helix chain 'L' and resid 228 through 253 removed outlier: 3.600A pdb=" N ARG L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY L 253 " --> pdb=" O ILE L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 263 Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.600A pdb=" N GLU M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 44 removed outlier: 3.639A pdb=" N TRP M 43 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 79 Processing helix chain 'M' and resid 83 through 90 Processing helix chain 'M' and resid 91 through 94 removed outlier: 3.631A pdb=" N LEU M 94 " --> pdb=" O LEU M 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 91 through 94' Processing helix chain 'M' and resid 100 through 104 removed outlier: 3.593A pdb=" N GLY M 104 " --> pdb=" O PRO M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 141 removed outlier: 3.616A pdb=" N ALA M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.683A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.549A pdb=" N GLU M 174 " --> pdb=" O SER M 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA M 175 " --> pdb=" O TRP M 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 171 through 175' Processing helix chain 'M' and resid 179 through 194 removed outlier: 3.717A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR M 194 " --> pdb=" O PHE M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.792A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.859A pdb=" N ARG M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR M 277 " --> pdb=" O PHE M 273 " (cutoff:3.500A) Proline residue: M 278 - end of helix Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 313 through 317 removed outlier: 3.554A pdb=" N ALA M 316 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 325 Processing helix chain 'a' and resid 3 through 10 removed outlier: 3.505A pdb=" N ILE a 7 " --> pdb=" O PHE a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.555A pdb=" N VAL a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR a 38 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 49 Processing helix chain 'b' and resid 12 through 45 removed outlier: 3.774A pdb=" N SER b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.519A pdb=" N TRP c 8 " --> pdb=" O TYR c 5 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 37 removed outlier: 3.671A pdb=" N VAL c 18 " --> pdb=" O ARG c 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 51 Processing helix chain 'd' and resid 12 through 45 Processing helix chain 'e' and resid 3 through 10 Processing helix chain 'e' and resid 12 through 37 removed outlier: 3.606A pdb=" N PHE e 25 " --> pdb=" O GLY e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 51 Processing helix chain 'f' and resid 12 through 45 Processing helix chain 'g' and resid 3 through 10 removed outlier: 3.545A pdb=" N TRP g 8 " --> pdb=" O TYR g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 37 removed outlier: 3.538A pdb=" N VAL g 18 " --> pdb=" O ARG g 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 50 Processing helix chain 'h' and resid 12 through 45 removed outlier: 3.681A pdb=" N VAL h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 10 removed outlier: 3.533A pdb=" N TRP i 8 " --> pdb=" O TYR i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 36 removed outlier: 3.837A pdb=" N VAL i 18 " --> pdb=" O ARG i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 51 removed outlier: 3.553A pdb=" N ALA i 51 " --> pdb=" O ALA i 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 45 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'k' and resid 12 through 37 removed outlier: 4.179A pdb=" N VAL k 18 " --> pdb=" O ARG k 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA k 19 " --> pdb=" O ARG k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 51 removed outlier: 3.585A pdb=" N ALA k 48 " --> pdb=" O PHE k 44 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 removed outlier: 3.680A pdb=" N VAL l 22 " --> pdb=" O GLU l 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 removed outlier: 3.574A pdb=" N TRP m 8 " --> pdb=" O TYR m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 37 removed outlier: 3.611A pdb=" N VAL m 18 " --> pdb=" O ARG m 14 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 51 removed outlier: 4.067A pdb=" N LEU m 46 " --> pdb=" O ASN m 42 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA m 47 " --> pdb=" O TRP m 43 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA m 48 " --> pdb=" O PHE m 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 removed outlier: 3.562A pdb=" N ALA n 16 " --> pdb=" O THR n 12 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU n 29 " --> pdb=" O SER n 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 10 removed outlier: 3.522A pdb=" N LYS o 6 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE o 7 " --> pdb=" O PHE o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 25 removed outlier: 3.742A pdb=" N VAL o 18 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA o 19 " --> pdb=" O ARG o 15 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 37 Processing helix chain 'p' and resid 12 through 45 removed outlier: 3.891A pdb=" N SER p 25 " --> pdb=" O SER p 21 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 50 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA3, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.360A pdb=" N GLY H 162 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU H 183 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL H 164 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 4.292A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 141 through 145 removed outlier: 6.750A pdb=" N GLN M 12 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.002A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 36 through 37 994 hydrogen bonds defined for protein. 2751 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: 2.91 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 6659 1.37 - 1.56: 14178 1.56 - 1.75: 23 1.75 - 1.94: 132 1.94 - 2.13: 107 Bond restraints: 21099 Sorted by residual: bond pdb=" N PRO H 54 " pdb=" CD PRO H 54 " ideal model delta sigma weight residual 1.473 1.629 -0.156 1.40e-02 5.10e+03 1.23e+02 bond pdb=" C21 SPN 8 102 " pdb=" C22 SPN 8 102 " ideal model delta sigma weight residual 1.531 1.339 0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" C21 SPN p 103 " pdb=" C22 SPN p 103 " ideal model delta sigma weight residual 1.531 1.339 0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" C21 SPN 9 101 " pdb=" C22 SPN 9 101 " ideal model delta sigma weight residual 1.531 1.339 0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C21 SPN n 102 " pdb=" C22 SPN n 102 " ideal model delta sigma weight residual 1.531 1.339 0.192 2.00e-02 2.50e+03 9.19e+01 ... (remaining 21094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 27958 4.14 - 8.29: 799 8.29 - 12.43: 180 12.43 - 16.58: 118 16.58 - 20.72: 10 Bond angle restraints: 29065 Sorted by residual: angle pdb=" N THR C 124 " pdb=" CA THR C 124 " pdb=" C THR C 124 " ideal model delta sigma weight residual 109.72 91.79 17.93 1.60e+00 3.91e-01 1.26e+02 angle pdb=" N PHE 9 4 " pdb=" CA PHE 9 4 " pdb=" C PHE 9 4 " ideal model delta sigma weight residual 113.97 103.22 10.75 1.28e+00 6.10e-01 7.06e+01 angle pdb=" N GLU o 45 " pdb=" CA GLU o 45 " pdb=" C GLU o 45 " ideal model delta sigma weight residual 113.55 103.00 10.55 1.26e+00 6.30e-01 7.01e+01 angle pdb=" N TYR L 165 " pdb=" CA TYR L 165 " pdb=" C TYR L 165 " ideal model delta sigma weight residual 111.87 101.51 10.36 1.41e+00 5.03e-01 5.40e+01 angle pdb=" N PHE C 6 " pdb=" CA PHE C 6 " pdb=" C PHE C 6 " ideal model delta sigma weight residual 113.72 104.48 9.24 1.30e+00 5.92e-01 5.05e+01 ... (remaining 29060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 10661 34.80 - 69.59: 738 69.59 - 104.39: 49 104.39 - 139.18: 7 139.18 - 173.98: 5 Dihedral angle restraints: 11460 sinusoidal: 5224 harmonic: 6236 Sorted by residual: dihedral pdb=" C1 BCL 8 101 " pdb=" CGA BCL 8 101 " pdb=" O2A BCL 8 101 " pdb=" CBA BCL 8 101 " ideal model delta sinusoidal sigma weight residual 180.00 18.21 161.79 1 6.00e+00 2.78e-02 5.20e+02 dihedral pdb=" CBD BCL 7 101 " pdb=" CGD BCL 7 101 " pdb=" O2D BCL 7 101 " pdb=" CED BCL 7 101 " ideal model delta sinusoidal sigma weight residual -180.00 -76.50 -103.50 1 5.00e+00 4.00e-02 4.74e+02 dihedral pdb=" C1 BCL j 101 " pdb=" CGA BCL j 101 " pdb=" O2A BCL j 101 " pdb=" CBA BCL j 101 " ideal model delta sinusoidal sigma weight residual 180.00 45.80 134.20 1 6.00e+00 2.78e-02 4.53e+02 ... (remaining 11457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.519: 2866 0.519 - 1.039: 1 1.039 - 1.558: 0 1.558 - 2.078: 0 2.078 - 2.597: 20 Chirality restraints: 2887 Sorted by residual: chirality pdb=" C22 SPN g 103 " pdb=" C21 SPN g 103 " pdb=" C23 SPN g 103 " pdb=" CM7 SPN g 103 " both_signs ideal model delta sigma weight residual False -2.58 0.02 -2.60 2.00e-01 2.50e+01 1.69e+02 chirality pdb=" C22 SPN i 103 " pdb=" C21 SPN i 103 " pdb=" C23 SPN i 103 " pdb=" CM7 SPN i 103 " both_signs ideal model delta sigma weight residual False -2.58 0.01 -2.59 2.00e-01 2.50e+01 1.68e+02 chirality pdb=" C22 SPN a 104 " pdb=" C21 SPN a 104 " pdb=" C23 SPN a 104 " pdb=" CM7 SPN a 104 " both_signs ideal model delta sigma weight residual False -2.58 0.00 -2.58 2.00e-01 2.50e+01 1.66e+02 ... (remaining 2884 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL l 101 " -0.367 1.50e-02 4.44e+03 3.09e-01 2.12e+03 pdb=" C2 BCL l 101 " 0.537 1.50e-02 4.44e+03 pdb=" C3 BCL l 101 " 0.114 1.50e-02 4.44e+03 pdb=" C4 BCL l 101 " -0.135 1.50e-02 4.44e+03 pdb=" C5 BCL l 101 " -0.150 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL d 101 " -0.366 1.50e-02 4.44e+03 3.08e-01 2.11e+03 pdb=" C2 BCL d 101 " 0.537 1.50e-02 4.44e+03 pdb=" C3 BCL d 101 " 0.113 1.50e-02 4.44e+03 pdb=" C4 BCL d 101 " -0.132 1.50e-02 4.44e+03 pdb=" C5 BCL d 101 " -0.151 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 301 " 0.359 1.50e-02 4.44e+03 3.03e-01 2.04e+03 pdb=" C2 BCL L 301 " -0.527 1.50e-02 4.44e+03 pdb=" C3 BCL L 301 " -0.111 1.50e-02 4.44e+03 pdb=" C4 BCL L 301 " 0.158 1.50e-02 4.44e+03 pdb=" C5 BCL L 301 " 0.121 1.50e-02 4.44e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 13 2.34 - 2.98: 8948 2.98 - 3.62: 27228 3.62 - 4.26: 47425 4.26 - 4.90: 77856 Nonbonded interactions: 161470 Sorted by model distance: nonbonded pdb=" O HIS a 40 " pdb=" NH2 ARG b 45 " model vdw 1.703 3.120 nonbonded pdb=" OE2 GLU M 235 " pdb="FE FE M 401 " model vdw 2.058 2.260 nonbonded pdb=" CD ARG H 117 " pdb=" OD2 ASP H 234 " model vdw 2.154 3.440 nonbonded pdb=" OG SER C 82 " pdb=" OD1 ASP C 114 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU M 24 " pdb=" NZ LYS M 142 " model vdw 2.177 3.120 ... (remaining 161465 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 '0' and resid 5 through 48) selection = (chain '8' and resid 5 through 48) selection = (chain 'b' and resid 5 through 48) selection = (chain 'd' and resid 5 through 48) selection = (chain 'f' and resid 5 through 48) selection = (chain 'h' and resid 5 through 48) selection = (chain 'j' and resid 5 through 48) selection = (chain 'l' and resid 5 through 48) selection = (chain 'n' and resid 5 through 48) selection = (chain 'p' and resid 5 through 48) } ncs_group { reference = (chain '7' and resid 1 through 51) selection = (chain '9' and resid 1 through 51) selection = (chain 'a' and resid 1 through 51) selection = (chain 'c' and resid 1 through 51) selection = (chain 'e' and resid 1 through 51) selection = (chain 'g' and resid 1 through 51) selection = (chain 'i' and resid 1 through 51) selection = (chain 'k' and resid 1 through 51) selection = (chain 'm' and resid 1 through 51) selection = (chain 'o' and resid 1 through 51) } 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: 1.850 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.026 0.406 21126 Z= 1.705 Angle : 1.836 20.721 29065 Z= 0.769 Chirality : 0.228 2.597 2887 Planarity : 0.030 0.327 3544 Dihedral : 21.081 173.980 7430 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.94 % Allowed : 10.67 % Favored : 88.39 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.16 % 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: 0.39 (0.18), residues: 2112 helix: 1.32 (0.15), residues: 1218 sheet: 0.17 (1.13), residues: 21 loop : -1.30 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 8 TYR 0.032 0.002 TYR C 113 PHE 0.025 0.002 PHE H 55 TRP 0.030 0.002 TRP o 43 HIS 0.012 0.002 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.02190 (21099) covalent geometry : angle 1.83650 (29065) hydrogen bonds : bond 0.19360 ( 992) hydrogen bonds : angle 5.48137 ( 2751) Misc. bond : bond 0.36950 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 101 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6776 (p) REVERT: H 237 MET cc_start: 0.9022 (mtt) cc_final: 0.8798 (mtm) REVERT: L 24 ASP cc_start: 0.8898 (t0) cc_final: 0.8675 (t0) REVERT: a 45 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: b 21 SER cc_start: 0.7921 (t) cc_final: 0.7467 (p) outliers start: 17 outliers final: 7 residues processed: 216 average time/residue: 0.6336 time to fit residues: 154.6400 Evaluate side-chains 188 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain j residue 18 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 20 GLN g 50 ASN o 20 GLN o 40 HIS p 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095915 restraints weight = 23194.684| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.57 r_work: 0.2920 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 21126 Z= 0.165 Angle : 0.810 16.323 29065 Z= 0.324 Chirality : 0.041 0.193 2887 Planarity : 0.005 0.061 3544 Dihedral : 19.004 179.869 3658 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.82 (0.18), residues: 2112 helix: 1.69 (0.15), residues: 1250 sheet: -0.35 (0.94), residues: 27 loop : -1.26 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 174 TYR 0.030 0.002 TYR L 165 PHE 0.020 0.002 PHE M 158 TRP 0.019 0.002 TRP C 285 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00387 (21099) covalent geometry : angle 0.81012 (29065) hydrogen bonds : bond 0.07866 ( 992) hydrogen bonds : angle 4.03537 ( 2751) Misc. bond : bond 0.04070 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7195 (mmt) cc_final: 0.6550 (mmm) REVERT: 7 30 MET cc_start: 0.6972 (ptm) cc_final: 0.6763 (tmm) REVERT: H 234 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8336 (t0) REVERT: L 83 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: L 217 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7451 (t80) REVERT: b 21 SER cc_start: 0.7956 (t) cc_final: 0.7514 (p) REVERT: c 39 GLU cc_start: 0.8179 (tt0) cc_final: 0.7800 (tp30) REVERT: l 18 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7775 (tm-30) outliers start: 41 outliers final: 20 residues processed: 203 average time/residue: 0.5704 time to fit residues: 131.5670 Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain a residue 2 SER Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 ASN g 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099957 restraints weight = 23337.881| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.62 r_work: 0.2977 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 21126 Z= 0.120 Angle : 0.664 13.861 29065 Z= 0.267 Chirality : 0.037 0.133 2887 Planarity : 0.004 0.055 3544 Dihedral : 17.062 179.944 3647 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 2.56 % Allowed : 12.72 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.31 (0.18), residues: 2112 helix: 2.18 (0.15), residues: 1228 sheet: -0.20 (0.77), residues: 37 loop : -1.11 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 115 TYR 0.014 0.001 TYR L 165 PHE 0.016 0.001 PHE M 158 TRP 0.015 0.001 TRP C 285 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00260 (21099) covalent geometry : angle 0.66392 (29065) hydrogen bonds : bond 0.05900 ( 992) hydrogen bonds : angle 3.66468 ( 2751) Misc. bond : bond 0.02864 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7144 (mmt) cc_final: 0.6439 (mmm) REVERT: C 144 MET cc_start: 0.8918 (mmt) cc_final: 0.8512 (mmt) REVERT: C 297 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: H 234 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8372 (t0) REVERT: L 24 ASP cc_start: 0.8789 (t0) cc_final: 0.8580 (t0) REVERT: L 83 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: M 273 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7812 (t80) REVERT: a 2 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7554 (m) REVERT: b 21 SER cc_start: 0.8079 (t) cc_final: 0.7677 (p) REVERT: c 39 GLU cc_start: 0.8073 (tt0) cc_final: 0.7697 (tp30) REVERT: l 18 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7667 (tm-30) outliers start: 46 outliers final: 14 residues processed: 212 average time/residue: 0.5826 time to fit residues: 140.7360 Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 38 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain a residue 2 SER Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 105 optimal weight: 0.0970 chunk 67 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 0.0170 chunk 60 optimal weight: 0.0270 chunk 194 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 HIS g 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095474 restraints weight = 23342.217| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.56 r_work: 0.2901 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 21126 Z= 0.159 Angle : 0.754 15.268 29065 Z= 0.304 Chirality : 0.041 0.174 2887 Planarity : 0.004 0.060 3544 Dihedral : 17.152 179.979 3642 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 2.72 % Allowed : 12.94 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.11 (0.18), residues: 2112 helix: 2.03 (0.15), residues: 1230 sheet: -0.29 (0.75), residues: 37 loop : -1.24 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 15 TYR 0.023 0.002 TYR L 165 PHE 0.022 0.002 PHE M 158 TRP 0.013 0.001 TRP C 285 HIS 0.013 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00369 (21099) covalent geometry : angle 0.75394 (29065) hydrogen bonds : bond 0.07640 ( 992) hydrogen bonds : angle 3.79126 ( 2751) Misc. bond : bond 0.03994 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7220 (mmt) cc_final: 0.6542 (mmm) REVERT: C 113 TYR cc_start: 0.7549 (m-10) cc_final: 0.6621 (m-10) REVERT: H 234 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8310 (t0) REVERT: L 24 ASP cc_start: 0.9059 (t0) cc_final: 0.8855 (t0) REVERT: L 83 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: L 217 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7440 (t80) REVERT: a 2 SER cc_start: 0.7813 (p) cc_final: 0.7565 (m) REVERT: b 21 SER cc_start: 0.7999 (t) cc_final: 0.7588 (p) REVERT: c 39 GLU cc_start: 0.8196 (tt0) cc_final: 0.7805 (tp30) REVERT: f 19 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7883 (tt) REVERT: l 18 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7726 (tm-30) outliers start: 49 outliers final: 23 residues processed: 207 average time/residue: 0.6214 time to fit residues: 146.5643 Evaluate side-chains 199 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain c residue 30 MET Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 20 GLN C 223 ASN ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN g 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096335 restraints weight = 22997.623| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.55 r_work: 0.2916 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 21126 Z= 0.149 Angle : 0.724 13.653 29065 Z= 0.294 Chirality : 0.040 0.171 2887 Planarity : 0.004 0.060 3544 Dihedral : 16.795 179.929 3642 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 13.17 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.16 (0.18), residues: 2112 helix: 2.08 (0.15), residues: 1230 sheet: -0.32 (0.75), residues: 37 loop : -1.23 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 88 TYR 0.021 0.002 TYR L 165 PHE 0.021 0.001 PHE M 158 TRP 0.013 0.001 TRP C 285 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00343 (21099) covalent geometry : angle 0.72411 (29065) hydrogen bonds : bond 0.07171 ( 992) hydrogen bonds : angle 3.69288 ( 2751) Misc. bond : bond 0.03911 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: C 115 ARG cc_start: 0.7922 (tpp80) cc_final: 0.6824 (tpp80) REVERT: C 314 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: H 234 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8312 (t0) REVERT: L 24 ASP cc_start: 0.9028 (t0) cc_final: 0.8783 (t0) REVERT: L 83 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: L 217 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7447 (t80) REVERT: M 139 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: M 273 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7749 (t80) REVERT: a 2 SER cc_start: 0.7835 (p) cc_final: 0.7596 (m) REVERT: b 21 SER cc_start: 0.7988 (t) cc_final: 0.7578 (p) REVERT: c 39 GLU cc_start: 0.8177 (tt0) cc_final: 0.7803 (tp30) REVERT: f 19 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7901 (tt) REVERT: k 3 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8168 (mttp) REVERT: l 18 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7756 (tm-30) outliers start: 47 outliers final: 21 residues processed: 202 average time/residue: 0.6436 time to fit residues: 148.3022 Evaluate side-chains 197 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 9 residue 38 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095352 restraints weight = 22986.919| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.32 r_work: 0.2978 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 21126 Z= 0.129 Angle : 0.671 13.101 29065 Z= 0.273 Chirality : 0.038 0.159 2887 Planarity : 0.004 0.057 3544 Dihedral : 16.333 179.927 3642 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 2.11 % Allowed : 13.78 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.35 (0.18), residues: 2112 helix: 2.23 (0.15), residues: 1230 sheet: -0.26 (0.74), residues: 37 loop : -1.16 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 88 TYR 0.016 0.001 TYR L 165 PHE 0.020 0.001 PHE M 158 TRP 0.013 0.001 TRP C 285 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00291 (21099) covalent geometry : angle 0.67142 (29065) hydrogen bonds : bond 0.06410 ( 992) hydrogen bonds : angle 3.57662 ( 2751) Misc. bond : bond 0.03517 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7231 (mmt) cc_final: 0.6605 (mmm) REVERT: C 115 ARG cc_start: 0.7842 (tpp80) cc_final: 0.6775 (tpp80) REVERT: H 234 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8299 (t0) REVERT: L 24 ASP cc_start: 0.8926 (t0) cc_final: 0.8686 (t0) REVERT: L 83 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: L 217 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7342 (t80) REVERT: M 70 ASN cc_start: 0.8407 (m-40) cc_final: 0.8168 (m-40) REVERT: M 139 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: M 273 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.7793 (t80) REVERT: b 21 SER cc_start: 0.8013 (t) cc_final: 0.7603 (p) REVERT: c 39 GLU cc_start: 0.8045 (tt0) cc_final: 0.7632 (tp30) REVERT: k 3 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8118 (mttp) REVERT: l 18 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7578 (tm-30) outliers start: 38 outliers final: 22 residues processed: 191 average time/residue: 0.6200 time to fit residues: 135.0256 Evaluate side-chains 195 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain c residue 30 MET Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 178 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 137 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 20 GLN g 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093325 restraints weight = 23215.084| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.29 r_work: 0.2858 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.252 21126 Z= 0.252 Angle : 0.904 14.259 29065 Z= 0.373 Chirality : 0.048 0.249 2887 Planarity : 0.005 0.064 3544 Dihedral : 17.740 179.841 3642 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.50 % Allowed : 13.61 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.70 (0.18), residues: 2112 helix: 1.63 (0.14), residues: 1243 sheet: -0.31 (0.88), residues: 27 loop : -1.35 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 88 TYR 0.026 0.003 TYR L 165 PHE 0.024 0.002 PHE M 158 TRP 0.013 0.002 TRP 8 28 HIS 0.016 0.002 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00630 (21099) covalent geometry : angle 0.90375 (29065) hydrogen bonds : bond 0.09695 ( 992) hydrogen bonds : angle 3.95556 ( 2751) Misc. bond : bond 0.05647 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 314 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: H 128 HIS cc_start: 0.7247 (m170) cc_final: 0.6999 (m170) REVERT: L 83 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: L 217 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7473 (t80) REVERT: b 21 SER cc_start: 0.8018 (t) cc_final: 0.7575 (p) REVERT: c 15 ARG cc_start: 0.8058 (mtt180) cc_final: 0.6714 (tmt170) REVERT: c 39 GLU cc_start: 0.8293 (tt0) cc_final: 0.7819 (tp30) REVERT: k 3 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8272 (mttp) REVERT: n 25 SER cc_start: 0.9007 (t) cc_final: 0.8675 (m) outliers start: 45 outliers final: 30 residues processed: 198 average time/residue: 0.6501 time to fit residues: 145.9218 Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain c residue 30 MET Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 205 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098868 restraints weight = 23233.121| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.45 r_work: 0.2952 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 21126 Z= 0.129 Angle : 0.683 12.966 29065 Z= 0.279 Chirality : 0.038 0.158 2887 Planarity : 0.004 0.058 3544 Dihedral : 16.661 179.924 3642 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.00 % Allowed : 14.11 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.18), residues: 2112 helix: 2.11 (0.15), residues: 1238 sheet: -0.32 (0.74), residues: 37 loop : -1.19 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 88 TYR 0.015 0.001 TYR L 165 PHE 0.020 0.001 PHE M 158 TRP 0.014 0.001 TRP C 285 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00284 (21099) covalent geometry : angle 0.68298 (29065) hydrogen bonds : bond 0.06664 ( 992) hydrogen bonds : angle 3.64490 ( 2751) Misc. bond : bond 0.04157 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7240 (mmt) cc_final: 0.6688 (mmm) REVERT: C 16 ASP cc_start: 0.7688 (m-30) cc_final: 0.7211 (m-30) REVERT: C 115 ARG cc_start: 0.7879 (tpp80) cc_final: 0.6814 (tpp80) REVERT: H 234 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8324 (t0) REVERT: L 217 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7415 (t80) REVERT: M 70 ASN cc_start: 0.8445 (m-40) cc_final: 0.8188 (m-40) REVERT: M 112 ASP cc_start: 0.7636 (t0) cc_final: 0.7291 (t70) REVERT: M 139 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: b 21 SER cc_start: 0.7977 (t) cc_final: 0.7567 (p) REVERT: c 39 GLU cc_start: 0.8156 (tt0) cc_final: 0.7720 (tp30) REVERT: k 3 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8144 (mttp) REVERT: l 18 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: l 24 MET cc_start: 0.8769 (mmp) cc_final: 0.8512 (mmm) outliers start: 36 outliers final: 22 residues processed: 196 average time/residue: 0.6158 time to fit residues: 137.9876 Evaluate side-chains 197 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100207 restraints weight = 23224.292| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.36 r_work: 0.2982 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 21126 Z= 0.120 Angle : 0.649 12.615 29065 Z= 0.265 Chirality : 0.037 0.156 2887 Planarity : 0.004 0.056 3544 Dihedral : 15.997 179.948 3642 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.06 % Allowed : 14.22 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.51 (0.18), residues: 2112 helix: 2.35 (0.15), residues: 1231 sheet: -0.17 (0.75), residues: 37 loop : -1.05 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.014 0.001 TYR L 165 PHE 0.018 0.001 PHE M 158 TRP 0.013 0.001 TRP d 47 HIS 0.010 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00265 (21099) covalent geometry : angle 0.64881 (29065) hydrogen bonds : bond 0.05938 ( 992) hydrogen bonds : angle 3.51003 ( 2751) Misc. bond : bond 0.03262 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: C 16 ASP cc_start: 0.7507 (m-30) cc_final: 0.7102 (m-30) REVERT: C 115 ARG cc_start: 0.7872 (tpp80) cc_final: 0.6820 (tpp80) REVERT: C 297 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8516 (tp30) REVERT: H 88 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8161 (ttt180) REVERT: H 234 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8337 (t0) REVERT: L 83 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: L 217 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7340 (t80) REVERT: M 70 ASN cc_start: 0.8408 (m-40) cc_final: 0.8197 (m-40) REVERT: M 273 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7797 (t80) REVERT: b 21 SER cc_start: 0.8021 (t) cc_final: 0.7622 (p) REVERT: c 39 GLU cc_start: 0.8107 (tt0) cc_final: 0.7688 (tp30) REVERT: k 3 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8130 (mttp) REVERT: l 18 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7558 (tm-30) outliers start: 37 outliers final: 22 residues processed: 200 average time/residue: 0.5927 time to fit residues: 134.9413 Evaluate side-chains 204 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 14 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095142 restraints weight = 23185.372| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.41 r_work: 0.2886 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.223 21126 Z= 0.213 Angle : 0.835 13.376 29065 Z= 0.344 Chirality : 0.045 0.226 2887 Planarity : 0.005 0.063 3544 Dihedral : 17.125 179.810 3642 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Rotamer: Outliers : 1.94 % Allowed : 14.44 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.97 (0.18), residues: 2112 helix: 1.85 (0.14), residues: 1245 sheet: -0.11 (0.90), residues: 27 loop : -1.24 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 88 TYR 0.023 0.002 TYR L 165 PHE 0.023 0.002 PHE M 158 TRP 0.012 0.002 TRP 8 28 HIS 0.015 0.002 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00523 (21099) covalent geometry : angle 0.83487 (29065) hydrogen bonds : bond 0.08804 ( 992) hydrogen bonds : angle 3.82436 ( 2751) Misc. bond : bond 0.05119 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: C 16 ASP cc_start: 0.7735 (m-30) cc_final: 0.7347 (m-30) REVERT: C 314 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7384 (pp20) REVERT: L 83 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: L 217 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7517 (t80) REVERT: b 21 SER cc_start: 0.8059 (t) cc_final: 0.7649 (p) REVERT: c 39 GLU cc_start: 0.8261 (tt0) cc_final: 0.7846 (tp30) REVERT: k 3 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8252 (mttp) REVERT: l 18 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7759 (tm-30) outliers start: 35 outliers final: 26 residues processed: 188 average time/residue: 0.6216 time to fit residues: 132.6841 Evaluate side-chains 196 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain n residue 21 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 85 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100402 restraints weight = 23218.877| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.39 r_work: 0.2971 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 21126 Z= 0.123 Angle : 0.658 12.500 29065 Z= 0.269 Chirality : 0.038 0.154 2887 Planarity : 0.004 0.056 3544 Dihedral : 16.169 179.973 3642 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 14.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.50 (0.18), residues: 2112 helix: 2.39 (0.15), residues: 1215 sheet: -0.26 (0.73), residues: 37 loop : -1.06 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.013 0.001 TYR L 165 PHE 0.019 0.001 PHE M 158 TRP 0.014 0.001 TRP C 285 HIS 0.010 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00267 (21099) covalent geometry : angle 0.65794 (29065) hydrogen bonds : bond 0.06188 ( 992) hydrogen bonds : angle 3.55938 ( 2751) Misc. bond : bond 0.03776 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8599.54 seconds wall clock time: 146 minutes 37.14 seconds (8797.14 seconds total)