Starting phenix.real_space_refine on Sat Jul 4 12:16:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltu_63381/07_2026/9ltu_63381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltu_63381/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ltu_63381/07_2026/9ltu_63381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltu_63381/07_2026/9ltu_63381.map" model { file = "/net/cci-nas-00/data/ceres_data/9ltu_63381/07_2026/9ltu_63381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltu_63381/07_2026/9ltu_63381.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 30 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 303 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'BCL': 2, 'BPH': 1, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 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: 4.54, per 1000 atoms: 0.22 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: 2.23 Conformation dependent library (CDL) restraints added in 610.7 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: 0.46 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: 2.72 Time building geometry restraints manager: 2.72 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: 27999 4.14 - 8.29: 758 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: 747 69.59 - 104.39: 45 104.39 - 139.18: 7 139.18 - 173.98: 4 Dihedral angle restraints: 11464 sinusoidal: 5228 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 11461 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 3.000 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: 1.830 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.860 Find NCS groups from input model: 0.400 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.025 0.406 21126 Z= 1.690 Angle : 1.820 20.721 29065 Z= 0.765 Chirality : 0.228 2.597 2887 Planarity : 0.030 0.327 3544 Dihedral : 20.986 173.980 7434 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/Z covalent geometry : bond 0.02143 / 1.07 (21099) covalent geometry : angle 1.81991 / 0.76 (29065) hydrogen bonds : bond 0.19360 / 12.82 ( 992) hydrogen bonds : angle 5.48137 / 3.90 ( 2751) Misc. bond : bond 0.36950 / 24.28 ( 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 : 0.761 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: 0.6026 time to fit residues: 148.1958 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 : 0.723 ------------------------------------------------------------------------------- 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... g 50 ASN o 20 GLN o 40 HIS p 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096281 restraints weight = 23230.323| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.62 r_work: 0.2923 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 21126 Z= 0.168 Angle : 0.814 16.239 29065 Z= 0.325 Chirality : 0.042 0.191 2887 Planarity : 0.005 0.061 3544 Dihedral : 19.075 179.896 3662 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Rotamer: Outliers : 2.44 % Allowed : 13.00 % Favored : 84.56 % 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: 0.82 (0.18), residues: 2112 helix: 1.70 (0.15), residues: 1250 sheet: -0.34 (0.94), residues: 27 loop : -1.26 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 0 45 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 0.012 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (21099) covalent geometry : angle 0.81413 / 0.33 (29065) hydrogen bonds : bond 0.07803 / 5.21 ( 992) hydrogen bonds : angle 4.02315 / 2.84 ( 2751) Misc. bond : bond 0.04097 / 1.79 ( 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 222 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7189 (mmt) cc_final: 0.6519 (mmm) REVERT: 7 30 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6763 (tmm) REVERT: H 234 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8319 (t0) REVERT: L 24 ASP cc_start: 0.8972 (t0) cc_final: 0.8760 (t0) REVERT: L 83 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: L 217 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7404 (t80) REVERT: M 112 ASP cc_start: 0.7966 (t0) cc_final: 0.7766 (t0) REVERT: b 21 SER cc_start: 0.7941 (t) cc_final: 0.7497 (p) REVERT: c 39 GLU cc_start: 0.8175 (tt0) cc_final: 0.7795 (tp30) REVERT: l 18 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7754 (tm-30) outliers start: 44 outliers final: 21 residues processed: 202 average time/residue: 0.5767 time to fit residues: 133.0931 Evaluate side-chains 201 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 30 MET 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 Chi-restraints excluded: chain p residue 21 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: 0.6980 chunk 207 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN e 50 ASN g 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100774 restraints weight = 23523.730| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.73 r_work: 0.2988 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 21126 Z= 0.118 Angle : 0.654 14.235 29065 Z= 0.264 Chirality : 0.037 0.133 2887 Planarity : 0.004 0.055 3544 Dihedral : 17.188 179.992 3651 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 2.28 % Allowed : 12.89 % Favored : 84.83 % 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: 1.33 (0.18), residues: 2112 helix: 2.21 (0.15), residues: 1222 sheet: -0.18 (0.77), residues: 37 loop : -1.12 (0.20), residues: 853 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 L 217 TRP 0.016 0.001 TRP C 285 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21099) covalent geometry : angle 0.65364 / 0.26 (29065) hydrogen bonds : bond 0.05799 / 3.88 ( 992) hydrogen bonds : angle 3.64426 / 2.55 ( 2751) Misc. bond : bond 0.02578 / 1.15 ( 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 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7125 (mmt) cc_final: 0.6423 (mmm) REVERT: C 115 ARG cc_start: 0.7925 (tpp80) cc_final: 0.6715 (tpp80) REVERT: C 144 MET cc_start: 0.8928 (mmt) cc_final: 0.8519 (mmt) REVERT: C 297 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8580 (tp30) REVERT: H 234 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8358 (t0) REVERT: L 83 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: a 2 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7542 (m) REVERT: b 21 SER cc_start: 0.8088 (t) cc_final: 0.7688 (p) REVERT: c 39 GLU cc_start: 0.8062 (tt0) cc_final: 0.7703 (tp30) REVERT: l 18 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: o 26 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7368 (tt) outliers start: 41 outliers final: 11 residues processed: 208 average time/residue: 0.6024 time to fit residues: 142.9164 Evaluate side-chains 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 o residue 26 LEU Chi-restraints excluded: chain p residue 11 LEU Chi-restraints excluded: chain p residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 105 optimal weight: 0.0570 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3598 r_free = 0.3598 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095513 restraints weight = 23351.678| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.43 r_work: 0.2907 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 21126 Z= 0.174 Angle : 0.779 14.962 29065 Z= 0.316 Chirality : 0.042 0.183 2887 Planarity : 0.005 0.060 3544 Dihedral : 17.400 179.998 3646 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 2.83 % Allowed : 13.06 % 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: 1.02 (0.18), residues: 2112 helix: 1.89 (0.15), residues: 1242 sheet: -0.29 (0.76), residues: 37 loop : -1.22 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 88 TYR 0.025 0.002 TYR L 165 PHE 0.022 0.002 PHE M 158 TRP 0.013 0.002 TRP C 285 HIS 0.014 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (21099) covalent geometry : angle 0.77879 / 0.32 (29065) hydrogen bonds : bond 0.08006 / 5.34 ( 992) hydrogen bonds : angle 3.83574 / 2.69 ( 2751) Misc. bond : bond 0.04209 / 1.81 ( 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: 51 poor density : 171 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7250 (mmt) cc_final: 0.6553 (mmm) REVERT: C 113 TYR cc_start: 0.7484 (m-10) cc_final: 0.6552 (m-10) REVERT: C 114 ASP cc_start: 0.6289 (p0) cc_final: 0.5953 (p0) REVERT: L 24 ASP cc_start: 0.8999 (t0) cc_final: 0.8789 (t0) REVERT: L 83 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: L 217 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7445 (t80) REVERT: M 112 ASP cc_start: 0.7938 (t0) cc_final: 0.7673 (t0) REVERT: b 21 SER cc_start: 0.8003 (t) cc_final: 0.7591 (p) REVERT: c 39 GLU cc_start: 0.8188 (tt0) cc_final: 0.7824 (tp30) REVERT: f 19 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7914 (tt) REVERT: l 18 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7711 (tm-30) outliers start: 51 outliers final: 26 residues processed: 207 average time/residue: 0.5632 time to fit residues: 133.4676 Evaluate side-chains 200 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 7 residue 17 PHE Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 38 THR 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 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 Chi-restraints excluded: chain p residue 43 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 193 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3646 r_free = 0.3646 target = 0.140190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100052 restraints weight = 23263.407| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.54 r_work: 0.2972 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 21126 Z= 0.121 Angle : 0.656 12.888 29065 Z= 0.266 Chirality : 0.037 0.155 2887 Planarity : 0.004 0.055 3544 Dihedral : 16.402 179.987 3646 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 1.94 % Allowed : 14.06 % Favored : 84.00 % 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: 1.40 (0.18), residues: 2112 helix: 2.29 (0.15), residues: 1217 sheet: -0.25 (0.74), residues: 37 loop : -1.10 (0.20), residues: 858 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 0.019 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/Z covalent geometry : bond 0.00268 / 0.12 (21099) covalent geometry : angle 0.65647 / 0.27 (29065) hydrogen bonds : bond 0.05979 / 4.00 ( 992) hydrogen bonds : angle 3.57021 / 2.49 ( 2751) Misc. bond : bond 0.03049 / 1.38 ( 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 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7129 (mmt) cc_final: 0.6392 (mmm) REVERT: C 115 ARG cc_start: 0.7863 (tpp80) cc_final: 0.6829 (tpp80) REVERT: H 234 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8369 (t0) REVERT: L 24 ASP cc_start: 0.8915 (t0) cc_final: 0.8689 (t0) REVERT: L 83 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: L 217 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7399 (t80) REVERT: M 70 ASN cc_start: 0.8415 (m-40) cc_final: 0.8208 (m-40) REVERT: M 273 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7820 (t80) REVERT: b 21 SER cc_start: 0.8074 (t) cc_final: 0.7671 (p) REVERT: c 39 GLU cc_start: 0.8115 (tt0) cc_final: 0.7732 (tp30) REVERT: j 18 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: l 18 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7643 (tm-30) outliers start: 35 outliers final: 15 residues processed: 200 average time/residue: 0.5740 time to fit residues: 131.1791 Evaluate side-chains 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU 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 273 PHE Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain j residue 18 GLU 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 43 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096204 restraints weight = 23078.528| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.34 r_work: 0.2904 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 21126 Z= 0.169 Angle : 0.763 13.906 29065 Z= 0.310 Chirality : 0.041 0.180 2887 Planarity : 0.004 0.059 3544 Dihedral : 16.949 179.867 3646 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 2.61 % Allowed : 13.22 % Favored : 84.17 % 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: 1.10 (0.18), residues: 2112 helix: 2.01 (0.15), residues: 1230 sheet: -0.31 (0.74), residues: 37 loop : -1.22 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 88 TYR 0.023 0.002 TYR L 165 PHE 0.022 0.002 PHE M 158 TRP 0.012 0.002 TRP e 43 HIS 0.014 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (21099) covalent geometry : angle 0.76320 / 0.31 (29065) hydrogen bonds : bond 0.07845 / 5.23 ( 992) hydrogen bonds : angle 3.74326 / 2.62 ( 2751) Misc. bond : bond 0.04285 / 1.85 ( 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 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: C 113 TYR cc_start: 0.7566 (m-10) cc_final: 0.6521 (m-10) REVERT: C 115 ARG cc_start: 0.7896 (tpp80) cc_final: 0.6784 (tpp80) REVERT: C 314 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7357 (pp20) REVERT: L 24 ASP cc_start: 0.9052 (t0) cc_final: 0.8781 (t0) REVERT: L 83 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: L 217 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7474 (t80) REVERT: M 273 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7768 (t80) REVERT: b 21 SER cc_start: 0.7958 (t) cc_final: 0.7541 (p) REVERT: c 39 GLU cc_start: 0.8196 (tt0) cc_final: 0.7838 (tp30) REVERT: f 19 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7908 (tt) REVERT: l 18 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7763 (tm-30) outliers start: 47 outliers final: 26 residues processed: 197 average time/residue: 0.5742 time to fit residues: 129.0144 Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LEU Chi-restraints excluded: chain 0 residue 38 HIS Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 38 THR 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 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 f residue 19 LEU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain j residue 18 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 178 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3623 r_free = 0.3623 target = 0.138399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098932 restraints weight = 23313.685| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.43 r_work: 0.2957 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 21126 Z= 0.133 Angle : 0.680 13.136 29065 Z= 0.277 Chirality : 0.038 0.166 2887 Planarity : 0.004 0.057 3544 Dihedral : 16.479 179.956 3646 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 2.28 % Allowed : 13.78 % Favored : 83.94 % 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: 1.30 (0.18), residues: 2112 helix: 2.18 (0.15), residues: 1230 sheet: -0.33 (0.73), residues: 37 loop : -1.15 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.017 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/Z covalent geometry : bond 0.00298 / 0.13 (21099) covalent geometry : angle 0.68001 / 0.28 (29065) hydrogen bonds : bond 0.06625 / 4.43 ( 992) hydrogen bonds : angle 3.60297 / 2.51 ( 2751) Misc. bond : bond 0.03844 / 1.73 ( 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 209 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7245 (mmt) cc_final: 0.6608 (mmm) REVERT: C 113 TYR cc_start: 0.7605 (m-10) cc_final: 0.6468 (m-10) REVERT: C 114 ASP cc_start: 0.6328 (p0) cc_final: 0.6016 (p0) REVERT: C 115 ARG cc_start: 0.7864 (tpp80) cc_final: 0.6779 (tpp80) REVERT: C 314 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: H 234 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8326 (t0) REVERT: L 24 ASP cc_start: 0.9021 (t0) cc_final: 0.8754 (t0) REVERT: L 83 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: M 70 ASN cc_start: 0.8437 (m-40) cc_final: 0.8179 (m-40) REVERT: M 273 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7790 (t80) REVERT: b 21 SER cc_start: 0.8012 (t) cc_final: 0.7601 (p) REVERT: c 39 GLU cc_start: 0.8115 (tt0) cc_final: 0.7742 (tp30) REVERT: f 19 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7820 (tt) REVERT: l 18 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7639 (tm-30) outliers start: 41 outliers final: 25 residues processed: 196 average time/residue: 0.6127 time to fit residues: 137.0204 Evaluate side-chains 197 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 C residue 110 VAL Chi-restraints excluded: chain C residue 314 GLU 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 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 248 CYS Chi-restraints excluded: chain L residue 257 THR 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 f residue 19 LEU Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain o residue 26 LEU 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: 0.0010 chunk 11 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3663 r_free = 0.3663 target = 0.141728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102328 restraints weight = 23202.675| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.50 r_work: 0.3010 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21126 Z= 0.109 Angle : 0.612 11.773 29065 Z= 0.249 Chirality : 0.036 0.140 2887 Planarity : 0.004 0.055 3544 Dihedral : 15.751 179.973 3646 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.83 % Allowed : 14.39 % Favored : 83.78 % 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: 1.62 (0.19), residues: 2112 helix: 2.46 (0.15), residues: 1223 sheet: -0.21 (0.72), residues: 37 loop : -1.02 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.011 0.001 TYR L 165 PHE 0.018 0.001 PHE M 158 TRP 0.013 0.001 TRP C 285 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21099) covalent geometry : angle 0.61240 / 0.25 (29065) hydrogen bonds : bond 0.05326 / 3.56 ( 992) hydrogen bonds : angle 3.42974 / 2.39 ( 2751) Misc. bond : bond 0.02879 / 1.32 ( 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 207 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: 0 24 MET cc_start: 0.7220 (mmt) cc_final: 0.6552 (mmm) REVERT: C 113 TYR cc_start: 0.7633 (m-10) cc_final: 0.6492 (m-10) REVERT: C 114 ASP cc_start: 0.6022 (p0) cc_final: 0.5636 (p0) REVERT: C 297 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8539 (tp30) REVERT: H 88 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8214 (tmm160) REVERT: H 234 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8331 (t0) REVERT: L 83 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: M 273 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7841 (t80) REVERT: b 21 SER cc_start: 0.8031 (t) cc_final: 0.7640 (p) REVERT: c 39 GLU cc_start: 0.7956 (tt0) cc_final: 0.7601 (tp30) REVERT: j 18 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: l 18 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: o 26 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6657 (tt) outliers start: 33 outliers final: 16 residues processed: 196 average time/residue: 0.6130 time to fit residues: 137.4629 Evaluate side-chains 196 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 80 VAL 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 j residue 18 GLU Chi-restraints excluded: chain l residue 18 GLU Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU 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: 0.0770 chunk 53 optimal weight: 0.0270 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3681 r_free = 0.3681 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103587 restraints weight = 23211.978| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.49 r_work: 0.3024 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 21126 Z= 0.103 Angle : 0.594 11.429 29065 Z= 0.242 Chirality : 0.036 0.134 2887 Planarity : 0.004 0.054 3544 Dihedral : 15.326 179.994 3646 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.50 % Allowed : 14.67 % Favored : 83.83 % 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: 1.78 (0.19), residues: 2112 helix: 2.53 (0.15), residues: 1232 sheet: -0.07 (0.73), residues: 37 loop : -0.89 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.010 0.001 TYR L 165 PHE 0.017 0.001 PHE M 158 TRP 0.013 0.001 TRP d 47 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (21099) covalent geometry : angle 0.59408 / 0.24 (29065) hydrogen bonds : bond 0.04959 / 3.31 ( 992) hydrogen bonds : angle 3.35596 / 2.33 ( 2751) Misc. bond : bond 0.02475 / 1.14 ( 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 206 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 114 ASP cc_start: 0.5967 (p0) cc_final: 0.5508 (p0) REVERT: C 144 MET cc_start: 0.8734 (mmt) cc_final: 0.8250 (mmt) REVERT: C 297 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8578 (tp30) REVERT: H 88 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8203 (tmm160) REVERT: H 234 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8350 (t0) REVERT: L 83 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: L 217 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7328 (t80) REVERT: L 250 ILE cc_start: 0.7887 (tt) cc_final: 0.7633 (tp) REVERT: M 19 LEU cc_start: 0.7939 (mt) cc_final: 0.7701 (mm) REVERT: M 273 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7860 (t80) REVERT: b 21 SER cc_start: 0.8010 (t) cc_final: 0.7627 (p) REVERT: c 39 GLU cc_start: 0.7903 (tt0) cc_final: 0.7553 (tp30) REVERT: l 24 MET cc_start: 0.8732 (mmp) cc_final: 0.8519 (mmm) outliers start: 27 outliers final: 14 residues processed: 197 average time/residue: 0.6125 time to fit residues: 137.7206 Evaluate side-chains 196 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 297 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 181 LEU 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 M residue 80 VAL Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain c residue 30 MET Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 11 LEU 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: 7.9990 chunk 196 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3619 r_free = 0.3619 target = 0.138008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099355 restraints weight = 23230.819| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.41 r_work: 0.2947 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 21126 Z= 0.146 Angle : 0.699 12.827 29065 Z= 0.285 Chirality : 0.040 0.173 2887 Planarity : 0.004 0.055 3544 Dihedral : 16.019 179.982 3646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 15.00 % Favored : 83.39 % 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: 1.48 (0.18), residues: 2112 helix: 2.27 (0.15), residues: 1239 sheet: -0.12 (0.73), residues: 37 loop : -1.01 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.019 0.002 TYR L 165 PHE 0.019 0.001 PHE M 158 TRP 0.012 0.001 TRP e 43 HIS 0.013 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (21099) covalent geometry : angle 0.69933 / 0.29 (29065) hydrogen bonds : bond 0.06931 / 4.62 ( 992) hydrogen bonds : angle 3.57267 / 2.49 ( 2751) Misc. bond : bond 0.03862 / 1.70 ( 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 201 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: C 115 ARG cc_start: 0.7774 (tpp80) cc_final: 0.6820 (tpp80) REVERT: H 234 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8347 (t0) REVERT: L 83 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: M 70 ASN cc_start: 0.8443 (m-40) cc_final: 0.8197 (m-40) REVERT: M 112 ASP cc_start: 0.7878 (t0) cc_final: 0.7626 (t70) REVERT: M 273 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7808 (t80) REVERT: b 21 SER cc_start: 0.8054 (t) cc_final: 0.7665 (p) REVERT: c 39 GLU cc_start: 0.8150 (tt0) cc_final: 0.7728 (tp30) REVERT: l 24 MET cc_start: 0.8787 (mmp) cc_final: 0.8504 (mmm) outliers start: 29 outliers final: 20 residues processed: 193 average time/residue: 0.6112 time to fit residues: 134.3916 Evaluate side-chains 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 355 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 275 VAL 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 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 85 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 204 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3624 r_free = 0.3624 target = 0.138384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098454 restraints weight = 23256.818| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.38 r_work: 0.2955 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 21126 Z= 0.136 Angle : 0.678 12.558 29065 Z= 0.276 Chirality : 0.039 0.166 2887 Planarity : 0.004 0.055 3544 Dihedral : 15.979 179.969 3646 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 1.56 % Allowed : 15.11 % Favored : 83.33 % 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: 1.47 (0.18), residues: 2112 helix: 2.27 (0.15), residues: 1238 sheet: -0.16 (0.73), residues: 37 loop : -1.03 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 88 TYR 0.016 0.001 TYR L 165 PHE 0.021 0.001 PHE L 217 TRP 0.012 0.001 TRP C 285 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (21099) covalent geometry : angle 0.67759 / 0.28 (29065) hydrogen bonds : bond 0.06625 / 4.42 ( 992) hydrogen bonds : angle 3.55796 / 2.47 ( 2751) Misc. bond : bond 0.03863 / 1.73 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8345.68 seconds wall clock time: 142 minutes 22.61 seconds (8542.61 seconds total)