Starting phenix.real_space_refine on Wed Mar 12 09:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9a_30310/03_2025/7c9a_30310.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Ca 3 9.91 5 P 27 5.49 5 S 39 5.16 5 C 4674 2.51 5 N 1341 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7590 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2375 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.27, per 1000 atoms: 0.83 Number of scatterers: 7590 At special positions: 0 Unit cell: (103.32, 84, 115.08, 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) Ca 3 19.99 S 39 16.00 P 27 15.00 O 1506 8.00 N 1341 7.00 C 4674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 49.6% alpha, 12.4% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.986A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.638A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 4.283A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 82' Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.740A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 removed outlier: 3.684A pdb=" N ASP A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.561A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 141 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.601A pdb=" N GLY A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 4.078A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 31 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.987A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.639A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.283A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.740A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.685A pdb=" N ASP B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.560A pdb=" N CYS B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 141 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.600A pdb=" N GLY B 151 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 209 removed outlier: 4.078A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 removed outlier: 3.568A pdb=" N ARG C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.986A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.679A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.639A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.554A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.284A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 82' Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.740A pdb=" N GLN C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.685A pdb=" N ASP C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.561A pdb=" N CYS C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.601A pdb=" N GLY C 151 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.523A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 removed outlier: 3.683A pdb=" N ASN C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 209 removed outlier: 4.079A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.521A pdb=" N MET C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.770A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.532A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 266 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.531A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 266 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 189 through 193 removed outlier: 3.591A pdb=" N THR C 266 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 236 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2235 1.33 - 1.45: 1238 1.45 - 1.57: 4158 1.57 - 1.69: 47 1.69 - 1.81: 63 Bond restraints: 7741 Sorted by residual: bond pdb=" O3A ANP A 403 " pdb=" PB ANP A 403 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 7736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 10443 4.18 - 8.37: 84 8.37 - 12.55: 7 12.55 - 16.74: 0 16.74 - 20.92: 3 Bond angle restraints: 10537 Sorted by residual: angle pdb=" PB ANP A 403 " pdb=" N3B ANP A 403 " pdb=" PG ANP A 403 " ideal model delta sigma weight residual 126.95 106.03 20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" CA GLU C 29 " pdb=" CB GLU C 29 " pdb=" CG GLU C 29 " ideal model delta sigma weight residual 114.10 122.93 -8.83 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 ... (remaining 10532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.29: 4390 29.29 - 58.58: 253 58.58 - 87.87: 63 87.87 - 117.16: 1 117.16 - 146.45: 6 Dihedral angle restraints: 4713 sinusoidal: 2058 harmonic: 2655 Sorted by residual: dihedral pdb=" CA ASP C 222 " pdb=" C ASP C 222 " pdb=" N SER C 223 " pdb=" CA SER C 223 " ideal model delta harmonic sigma weight residual -180.00 -61.85 -118.15 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP B 222 " pdb=" C ASP B 222 " pdb=" N SER B 223 " pdb=" CA SER B 223 " ideal model delta harmonic sigma weight residual -180.00 -61.86 -118.14 0 5.00e+00 4.00e-02 5.58e+02 dihedral pdb=" CA ASP A 222 " pdb=" C ASP A 222 " pdb=" N SER A 223 " pdb=" CA SER A 223 " ideal model delta harmonic sigma weight residual -180.00 -61.93 -118.07 0 5.00e+00 4.00e-02 5.58e+02 ... (remaining 4710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1010 0.063 - 0.126: 166 0.126 - 0.188: 18 0.188 - 0.251: 0 0.251 - 0.314: 3 Chirality restraints: 1197 Sorted by residual: chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' ANP A 403 " pdb=" C2' ANP A 403 " pdb=" C4' ANP A 403 " pdb=" O3' ANP A 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1194 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 166 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C PHE B 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 166 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C PHE C 166 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE C 166 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG C 167 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 166 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C PHE A 166 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE A 166 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 167 " -0.020 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 44 2.55 - 3.14: 5155 3.14 - 3.73: 10551 3.73 - 4.31: 15757 4.31 - 4.90: 26283 Nonbonded interactions: 57790 Sorted by model distance: nonbonded pdb=" CE1 PHE A 129 " pdb=" O ALA B 293 " model vdw 1.965 3.340 nonbonded pdb=" CE1 PHE B 129 " pdb=" O ALA C 293 " model vdw 2.003 3.340 nonbonded pdb=" CD1 PHE A 129 " pdb=" O ALA B 293 " model vdw 2.063 3.340 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.078 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.079 2.510 ... (remaining 57785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.520 Find NCS groups from input model: 0.370 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 7741 Z= 0.426 Angle : 1.036 20.922 10537 Z= 0.565 Chirality : 0.048 0.314 1197 Planarity : 0.005 0.039 1293 Dihedral : 19.518 146.452 3015 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.20), residues: 921 helix: -5.05 (0.06), residues: 387 sheet: 0.85 (0.48), residues: 120 loop : -2.66 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 199 PHE 0.019 0.002 PHE B 129 TYR 0.013 0.002 TYR C 315 ARG 0.006 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8107 (mmmt) REVERT: B 130 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7413 (ptp90) REVERT: B 156 LYS cc_start: 0.8757 (mttt) cc_final: 0.8307 (mtpt) REVERT: B 254 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7977 (mtp-110) REVERT: B 285 LYS cc_start: 0.9038 (pttt) cc_final: 0.8745 (ptmm) REVERT: C 237 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8069 (tt0) REVERT: C 285 LYS cc_start: 0.9110 (pttt) cc_final: 0.8877 (ptmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3327 time to fit residues: 93.3190 Evaluate side-chains 136 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 34 ASN B 242 GLN C 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101594 restraints weight = 10604.362| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.29 r_work: 0.2947 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7741 Z= 0.191 Angle : 0.587 8.083 10537 Z= 0.315 Chirality : 0.042 0.145 1197 Planarity : 0.004 0.030 1293 Dihedral : 17.483 151.855 1323 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.35 % Allowed : 13.90 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.22), residues: 921 helix: -3.59 (0.15), residues: 411 sheet: 0.90 (0.48), residues: 120 loop : -2.25 (0.25), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 138 PHE 0.012 0.001 PHE C 129 TYR 0.010 0.001 TYR A 159 ARG 0.006 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.852 Fit side-chains REVERT: A 29 GLU cc_start: 0.7741 (mp0) cc_final: 0.7184 (mm-30) REVERT: A 39 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7837 (mmmt) REVERT: A 247 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8483 (mtm-85) REVERT: A 258 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 156 LYS cc_start: 0.8805 (mttt) cc_final: 0.8440 (mtpt) REVERT: B 254 ARG cc_start: 0.8753 (ttp80) cc_final: 0.7923 (ttp-110) REVERT: B 285 LYS cc_start: 0.8726 (pttt) cc_final: 0.8466 (ptmm) REVERT: C 110 ASP cc_start: 0.8505 (m-30) cc_final: 0.8224 (m-30) REVERT: C 187 ASP cc_start: 0.8854 (t0) cc_final: 0.8448 (p0) REVERT: C 188 ASN cc_start: 0.8573 (m-40) cc_final: 0.8339 (m-40) REVERT: C 210 MET cc_start: 0.8727 (mtp) cc_final: 0.8216 (mtp) REVERT: C 254 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8109 (ttp-110) REVERT: C 285 LYS cc_start: 0.8758 (pttt) cc_final: 0.8395 (ptmm) outliers start: 10 outliers final: 2 residues processed: 173 average time/residue: 0.2934 time to fit residues: 62.6742 Evaluate side-chains 145 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098786 restraints weight = 10845.395| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.32 r_work: 0.2885 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7741 Z= 0.201 Angle : 0.526 6.859 10537 Z= 0.284 Chirality : 0.041 0.126 1197 Planarity : 0.004 0.029 1293 Dihedral : 15.825 146.094 1323 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.35 % Allowed : 16.87 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 921 helix: -2.10 (0.21), residues: 417 sheet: 0.77 (0.46), residues: 135 loop : -1.94 (0.27), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 138 PHE 0.011 0.002 PHE A 129 TYR 0.009 0.001 TYR C 315 ARG 0.007 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.180 Fit side-chains REVERT: A 29 GLU cc_start: 0.7706 (mp0) cc_final: 0.7490 (mm-30) REVERT: A 77 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 176 GLU cc_start: 0.8884 (tt0) cc_final: 0.8324 (mt-10) REVERT: A 247 ARG cc_start: 0.9047 (mtp85) cc_final: 0.8603 (mtm-85) REVERT: B 91 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 156 LYS cc_start: 0.8930 (mttt) cc_final: 0.8433 (mtmt) REVERT: B 254 ARG cc_start: 0.8837 (ttp80) cc_final: 0.7901 (ttp-110) REVERT: B 311 ILE cc_start: 0.9142 (mt) cc_final: 0.8823 (mm) REVERT: C 39 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7676 (mttm) REVERT: C 110 ASP cc_start: 0.8446 (m-30) cc_final: 0.8212 (m-30) REVERT: C 130 ARG cc_start: 0.7616 (ptt-90) cc_final: 0.6258 (tpt170) REVERT: C 176 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 285 LYS cc_start: 0.8704 (pttt) cc_final: 0.8474 (ptmm) outliers start: 10 outliers final: 10 residues processed: 170 average time/residue: 0.2933 time to fit residues: 62.4251 Evaluate side-chains 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.0030 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.102785 restraints weight = 10733.163| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.28 r_work: 0.2936 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7741 Z= 0.135 Angle : 0.466 5.649 10537 Z= 0.252 Chirality : 0.040 0.123 1197 Planarity : 0.003 0.027 1293 Dihedral : 15.230 146.580 1323 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.89 % Allowed : 18.22 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 921 helix: -1.03 (0.24), residues: 426 sheet: 0.83 (0.47), residues: 138 loop : -1.73 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.007 0.001 PHE B 126 TYR 0.006 0.001 TYR C 159 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.525 Fit side-chains REVERT: A 50 GLU cc_start: 0.8614 (mp0) cc_final: 0.8028 (mp0) REVERT: A 161 ASP cc_start: 0.8514 (t0) cc_final: 0.8187 (t0) REVERT: A 176 GLU cc_start: 0.8862 (tt0) cc_final: 0.8331 (mt-10) REVERT: A 247 ARG cc_start: 0.9040 (mtp85) cc_final: 0.8597 (mtm-85) REVERT: B 91 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 156 LYS cc_start: 0.8883 (mttt) cc_final: 0.8424 (mtmt) REVERT: B 311 ILE cc_start: 0.9141 (mt) cc_final: 0.8930 (mm) REVERT: C 94 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8636 (tp40) REVERT: C 130 ARG cc_start: 0.7470 (ptt-90) cc_final: 0.6519 (tpt170) REVERT: C 176 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 285 LYS cc_start: 0.8609 (pttt) cc_final: 0.8211 (ptmm) outliers start: 14 outliers final: 11 residues processed: 179 average time/residue: 0.3476 time to fit residues: 78.8947 Evaluate side-chains 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095882 restraints weight = 10804.234| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.25 r_work: 0.2822 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7741 Z= 0.331 Angle : 0.562 6.761 10537 Z= 0.301 Chirality : 0.043 0.136 1197 Planarity : 0.004 0.031 1293 Dihedral : 15.491 143.478 1323 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.83 % Allowed : 18.08 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 921 helix: -0.53 (0.26), residues: 417 sheet: 1.33 (0.48), residues: 132 loop : -1.70 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 138 PHE 0.016 0.002 PHE B 129 TYR 0.015 0.002 TYR C 315 ARG 0.006 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.913 Fit side-chains REVERT: A 50 GLU cc_start: 0.8764 (mp0) cc_final: 0.8258 (mp0) REVERT: A 205 TYR cc_start: 0.8779 (m-10) cc_final: 0.8480 (m-10) REVERT: A 247 ARG cc_start: 0.9011 (mtp85) cc_final: 0.8517 (mtm-85) REVERT: A 332 ASP cc_start: 0.8564 (m-30) cc_final: 0.8132 (p0) REVERT: B 91 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 156 LYS cc_start: 0.9014 (mttt) cc_final: 0.8506 (mtmt) REVERT: C 130 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.6526 (tpt170) REVERT: C 176 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 255 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (tt) REVERT: C 285 LYS cc_start: 0.8642 (pttt) cc_final: 0.8236 (ptmm) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.2664 time to fit residues: 52.3567 Evaluate side-chains 146 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101400 restraints weight = 10760.984| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.27 r_work: 0.2878 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7741 Z= 0.147 Angle : 0.468 5.325 10537 Z= 0.253 Chirality : 0.040 0.129 1197 Planarity : 0.003 0.024 1293 Dihedral : 15.124 146.789 1323 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.43 % Allowed : 19.57 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.28), residues: 921 helix: -0.07 (0.27), residues: 420 sheet: 1.10 (0.48), residues: 138 loop : -1.53 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 47 PHE 0.007 0.001 PHE B 129 TYR 0.004 0.001 TYR A 191 ARG 0.006 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.870 Fit side-chains REVERT: A 205 TYR cc_start: 0.8629 (m-10) cc_final: 0.8308 (m-10) REVERT: A 247 ARG cc_start: 0.9039 (mtp85) cc_final: 0.8516 (mtm-85) REVERT: B 91 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 156 LYS cc_start: 0.8869 (mttt) cc_final: 0.8387 (mtmt) REVERT: B 311 ILE cc_start: 0.9077 (mt) cc_final: 0.8738 (mm) REVERT: C 59 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 60 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7931 (mt) REVERT: C 94 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8567 (tp40) REVERT: C 130 ARG cc_start: 0.7529 (ptt-90) cc_final: 0.6597 (tpt170) REVERT: C 176 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 285 LYS cc_start: 0.8462 (pttt) cc_final: 0.8079 (ptmm) outliers start: 18 outliers final: 12 residues processed: 173 average time/residue: 0.2312 time to fit residues: 51.4720 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107313 restraints weight = 10669.816| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2876 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7741 Z= 0.204 Angle : 0.495 5.367 10537 Z= 0.266 Chirality : 0.041 0.128 1197 Planarity : 0.003 0.039 1293 Dihedral : 15.128 145.184 1323 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.29 % Allowed : 20.24 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.28), residues: 921 helix: 0.12 (0.27), residues: 420 sheet: 1.18 (0.48), residues: 138 loop : -1.45 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.012 0.001 PHE B 129 TYR 0.008 0.001 TYR C 315 ARG 0.010 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.891 Fit side-chains REVERT: A 176 GLU cc_start: 0.9010 (tt0) cc_final: 0.8800 (pt0) REVERT: A 205 TYR cc_start: 0.8654 (m-10) cc_final: 0.8243 (m-10) REVERT: A 247 ARG cc_start: 0.9016 (mtp85) cc_final: 0.8499 (mtm-85) REVERT: B 91 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 156 LYS cc_start: 0.8933 (mttt) cc_final: 0.8458 (mtmt) REVERT: B 311 ILE cc_start: 0.9121 (mt) cc_final: 0.8791 (mm) REVERT: C 59 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 60 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7913 (mt) REVERT: C 94 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8591 (tp40) REVERT: C 130 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.6594 (tpt170) REVERT: C 176 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 285 LYS cc_start: 0.8522 (pttt) cc_final: 0.8147 (ptmm) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.2241 time to fit residues: 46.0432 Evaluate side-chains 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 85 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104738 restraints weight = 10887.568| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.28 r_work: 0.2896 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7741 Z= 0.151 Angle : 0.467 5.288 10537 Z= 0.250 Chirality : 0.039 0.127 1197 Planarity : 0.003 0.038 1293 Dihedral : 14.904 145.628 1323 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.02 % Allowed : 20.51 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.28), residues: 921 helix: 0.37 (0.27), residues: 417 sheet: 1.16 (0.48), residues: 138 loop : -1.32 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 47 PHE 0.007 0.001 PHE A 126 TYR 0.005 0.001 TYR A 315 ARG 0.008 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.796 Fit side-chains REVERT: A 176 GLU cc_start: 0.8989 (tt0) cc_final: 0.8706 (pt0) REVERT: A 205 TYR cc_start: 0.8621 (m-10) cc_final: 0.8259 (m-10) REVERT: A 206 GLN cc_start: 0.8903 (mt0) cc_final: 0.8659 (tt0) REVERT: A 247 ARG cc_start: 0.9010 (mtp85) cc_final: 0.8564 (mtm-85) REVERT: B 91 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 156 LYS cc_start: 0.8921 (mttt) cc_final: 0.8471 (mtmt) REVERT: B 311 ILE cc_start: 0.9093 (mt) cc_final: 0.8750 (mm) REVERT: C 23 GLN cc_start: 0.7831 (mp10) cc_final: 0.7572 (mp10) REVERT: C 59 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 60 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7808 (mt) REVERT: C 94 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8567 (tp40) REVERT: C 130 ARG cc_start: 0.7335 (ptt-90) cc_final: 0.6622 (tpt170) REVERT: C 285 LYS cc_start: 0.8424 (pttt) cc_final: 0.8074 (ptmm) outliers start: 15 outliers final: 12 residues processed: 165 average time/residue: 0.2173 time to fit residues: 47.0473 Evaluate side-chains 161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.103993 restraints weight = 10973.556| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.27 r_work: 0.2949 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7741 Z= 0.150 Angle : 0.471 5.308 10537 Z= 0.251 Chirality : 0.040 0.125 1197 Planarity : 0.003 0.034 1293 Dihedral : 14.800 144.700 1323 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 21.32 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 921 helix: 0.50 (0.27), residues: 417 sheet: 1.17 (0.47), residues: 138 loop : -1.22 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 47 PHE 0.007 0.001 PHE A 126 TYR 0.006 0.001 TYR B 315 ARG 0.008 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.883 Fit side-chains REVERT: A 205 TYR cc_start: 0.8617 (m-10) cc_final: 0.8188 (m-10) REVERT: A 206 GLN cc_start: 0.8878 (mt0) cc_final: 0.8661 (tt0) REVERT: A 247 ARG cc_start: 0.9019 (mtp85) cc_final: 0.8581 (mtm-85) REVERT: B 91 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8111 (tm-30) REVERT: B 156 LYS cc_start: 0.8920 (mttt) cc_final: 0.8501 (mtmt) REVERT: B 311 ILE cc_start: 0.9138 (mt) cc_final: 0.8816 (mm) REVERT: C 23 GLN cc_start: 0.7881 (mp10) cc_final: 0.7440 (mp10) REVERT: C 59 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 60 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7846 (mt) REVERT: C 94 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8620 (tp40) REVERT: C 130 ARG cc_start: 0.7198 (ptt-90) cc_final: 0.6650 (tpt170) outliers start: 16 outliers final: 14 residues processed: 167 average time/residue: 0.2116 time to fit residues: 46.5543 Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.095589 restraints weight = 10898.967| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.40 r_work: 0.2808 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7741 Z= 0.311 Angle : 0.559 5.984 10537 Z= 0.296 Chirality : 0.043 0.199 1197 Planarity : 0.003 0.033 1293 Dihedral : 15.157 138.839 1323 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.02 % Allowed : 21.86 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 921 helix: 0.43 (0.27), residues: 402 sheet: 0.65 (0.55), residues: 111 loop : -1.03 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 138 PHE 0.016 0.002 PHE B 129 TYR 0.016 0.002 TYR B 315 ARG 0.007 0.000 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.713 Fit side-chains REVERT: A 77 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 247 ARG cc_start: 0.9028 (mtp85) cc_final: 0.8496 (mtm-85) REVERT: B 91 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 156 LYS cc_start: 0.8995 (mttt) cc_final: 0.8495 (mtmt) REVERT: C 59 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 130 ARG cc_start: 0.7475 (ptt-90) cc_final: 0.6641 (tpt170) outliers start: 15 outliers final: 11 residues processed: 146 average time/residue: 0.2742 time to fit residues: 53.2802 Evaluate side-chains 142 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.127328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.099891 restraints weight = 10660.846| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.36 r_work: 0.2887 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7741 Z= 0.159 Angle : 0.481 5.330 10537 Z= 0.256 Chirality : 0.040 0.126 1197 Planarity : 0.003 0.032 1293 Dihedral : 14.891 142.167 1323 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.75 % Allowed : 21.73 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 921 helix: 0.49 (0.27), residues: 417 sheet: 0.61 (0.55), residues: 111 loop : -1.24 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.007 0.001 PHE B 129 TYR 0.004 0.001 TYR A 232 ARG 0.007 0.000 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.91 seconds wall clock time: 83 minutes 32.16 seconds (5012.16 seconds total)