Starting phenix.real_space_refine on Wed Feb 12 09:57:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9a_30310/02_2025/7c9a_30310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9a_30310/02_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_30310/02_2025/7c9a_30310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9a_30310/02_2025/7c9a_30310.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9a_30310/02_2025/7c9a_30310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9a_30310/02_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-5592/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: 2.71, per 1000 atoms: 0.36 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 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: 2.27 Time building geometry restraints manager: 2.05 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: 0.000 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: 0.000 Extract box with map and model: 4.740 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.160 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 : 0.845 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: 0.3388 time to fit residues: 95.0082 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 : 0.956 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101592 restraints weight = 10604.362| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.29 r_work: 0.2929 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.808 Fit side-chains REVERT: A 29 GLU cc_start: 0.7743 (mp0) cc_final: 0.7187 (mm-30) REVERT: A 39 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7832 (mmmt) REVERT: A 247 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8471 (mtm-85) REVERT: A 258 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 156 LYS cc_start: 0.8801 (mttt) cc_final: 0.8428 (mtpt) REVERT: B 254 ARG cc_start: 0.8745 (ttp80) cc_final: 0.7912 (ttp-110) REVERT: B 285 LYS cc_start: 0.8705 (pttt) cc_final: 0.8445 (ptmm) REVERT: C 110 ASP cc_start: 0.8496 (m-30) cc_final: 0.8219 (m-30) REVERT: C 187 ASP cc_start: 0.8858 (t0) cc_final: 0.8445 (p0) REVERT: C 188 ASN cc_start: 0.8573 (m-40) cc_final: 0.8331 (m-40) REVERT: C 210 MET cc_start: 0.8730 (mtp) cc_final: 0.8212 (mtp) REVERT: C 254 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8095 (ttp-110) REVERT: C 285 LYS cc_start: 0.8742 (pttt) cc_final: 0.8379 (ptmm) outliers start: 10 outliers final: 2 residues processed: 173 average time/residue: 0.3033 time to fit residues: 64.2561 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 : 0.828 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101638 restraints weight = 10792.811| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.29 r_work: 0.2929 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7741 Z= 0.153 Angle : 0.502 6.373 10537 Z= 0.272 Chirality : 0.040 0.124 1197 Planarity : 0.003 0.027 1293 Dihedral : 15.693 144.684 1323 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.21 % Allowed : 16.73 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.56 (0.24), residues: 921 helix: -2.13 (0.21), residues: 417 sheet: 0.73 (0.46), residues: 135 loop : -1.97 (0.26), residues: 369 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 0.006 0.001 TYR C 159 ARG 0.007 0.000 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 185 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.919 Fit side-chains REVERT: A 29 GLU cc_start: 0.7648 (mp0) cc_final: 0.7414 (mm-30) REVERT: A 39 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7864 (mmmt) REVERT: A 77 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 176 GLU cc_start: 0.8883 (tt0) cc_final: 0.8314 (mt-10) REVERT: A 247 ARG cc_start: 0.9004 (mtp85) cc_final: 0.8564 (mtm-85) REVERT: B 91 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 156 LYS cc_start: 0.8873 (mttt) cc_final: 0.8418 (mtmt) REVERT: B 254 ARG cc_start: 0.8819 (ttp80) cc_final: 0.7871 (ttp-110) REVERT: C 39 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7640 (mttp) REVERT: C 94 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8556 (tp40) REVERT: C 110 ASP cc_start: 0.8446 (m-30) cc_final: 0.8204 (m-30) REVERT: C 130 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.6362 (tpt170) REVERT: C 285 LYS cc_start: 0.8729 (pttt) cc_final: 0.8499 (ptmm) outliers start: 9 outliers final: 8 residues processed: 180 average time/residue: 0.2761 time to fit residues: 62.0766 Evaluate side-chains 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 31 CYS 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 C residue 63 ILE 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: 0.0370 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.130471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104103 restraints weight = 10747.653| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.25 r_work: 0.2893 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7741 Z= 0.181 Angle : 0.487 6.126 10537 Z= 0.263 Chirality : 0.041 0.122 1197 Planarity : 0.003 0.028 1293 Dihedral : 15.267 145.905 1323 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.02 % Allowed : 18.76 % Favored : 79.22 % 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: -1.67 (0.26), residues: 921 helix: -1.10 (0.24), residues: 417 sheet: 0.83 (0.46), residues: 138 loop : -1.78 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.009 0.001 PHE B 129 TYR 0.008 0.001 TYR B 315 ARG 0.004 0.000 ARG B 130 *********************** 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 174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.649 Fit side-chains REVERT: A 39 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7957 (mmmt) REVERT: A 161 ASP cc_start: 0.8524 (t0) cc_final: 0.8122 (t0) REVERT: A 176 GLU cc_start: 0.8843 (tt0) cc_final: 0.8304 (mt-10) REVERT: A 205 TYR cc_start: 0.8574 (m-10) cc_final: 0.8192 (m-10) REVERT: A 247 ARG cc_start: 0.9039 (mtp85) cc_final: 0.8540 (mtm-85) REVERT: B 91 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 156 LYS cc_start: 0.8934 (mttt) cc_final: 0.8452 (mtmt) REVERT: C 94 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8628 (tp40) REVERT: C 110 ASP cc_start: 0.8477 (m-30) cc_final: 0.8270 (m-30) REVERT: C 130 ARG cc_start: 0.7566 (ptt-90) cc_final: 0.6456 (tpt170) REVERT: C 176 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 285 LYS cc_start: 0.8670 (pttt) cc_final: 0.8452 (ptmm) outliers start: 15 outliers final: 11 residues processed: 163 average time/residue: 0.2635 time to fit residues: 53.9392 Evaluate side-chains 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE 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 163 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0060 chunk 9 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.134781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.108434 restraints weight = 10636.286| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.27 r_work: 0.2913 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3666 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= 0.148 Angle : 0.459 5.705 10537 Z= 0.248 Chirality : 0.039 0.126 1197 Planarity : 0.003 0.026 1293 Dihedral : 14.979 146.189 1323 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 19.97 % Favored : 78.14 % 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: -0.99 (0.27), residues: 921 helix: -0.41 (0.25), residues: 426 sheet: 1.01 (0.47), residues: 138 loop : -1.56 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.008 0.001 PHE B 129 TYR 0.005 0.001 TYR B 315 ARG 0.004 0.000 ARG C 130 *********************** 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 181 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.822 Fit side-chains REVERT: A 39 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7904 (mmmt) REVERT: A 176 GLU cc_start: 0.8837 (tt0) cc_final: 0.8381 (mt-10) REVERT: A 205 TYR cc_start: 0.8574 (m-10) cc_final: 0.8148 (m-10) REVERT: A 206 GLN cc_start: 0.8916 (mt0) cc_final: 0.8693 (tt0) REVERT: A 247 ARG cc_start: 0.9020 (mtp85) cc_final: 0.8603 (mtm-85) REVERT: B 91 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 156 LYS cc_start: 0.8890 (mttt) cc_final: 0.8436 (mtmt) REVERT: C 94 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8622 (tp40) REVERT: C 101 GLN cc_start: 0.8334 (mt0) cc_final: 0.8121 (mt0) REVERT: C 110 ASP cc_start: 0.8362 (m-30) cc_final: 0.8152 (m-30) REVERT: C 130 ARG cc_start: 0.7396 (ptt-90) cc_final: 0.6498 (tpt170) REVERT: C 176 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 285 LYS cc_start: 0.8557 (pttt) cc_final: 0.8172 (ptmm) outliers start: 14 outliers final: 13 residues processed: 175 average time/residue: 0.2648 time to fit residues: 58.8463 Evaluate side-chains 169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 63 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 chunk 87 optimal weight: 0.0670 chunk 83 optimal weight: 0.9990 overall best weight: 1.0308 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.135366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109167 restraints weight = 10655.078| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.26 r_work: 0.2893 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7741 Z= 0.183 Angle : 0.472 5.843 10537 Z= 0.254 Chirality : 0.040 0.126 1197 Planarity : 0.003 0.029 1293 Dihedral : 14.990 145.109 1323 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 19.16 % Favored : 77.73 % 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: -0.64 (0.28), residues: 921 helix: -0.09 (0.26), residues: 429 sheet: 1.12 (0.47), residues: 138 loop : -1.40 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.009 0.001 PHE B 129 TYR 0.007 0.001 TYR B 315 ARG 0.005 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 183 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.801 Fit side-chains REVERT: A 39 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7925 (mmmt) REVERT: A 205 TYR cc_start: 0.8626 (m-10) cc_final: 0.8234 (m-10) REVERT: A 206 GLN cc_start: 0.8912 (mt0) cc_final: 0.8682 (tt0) REVERT: A 247 ARG cc_start: 0.9013 (mtp85) cc_final: 0.8486 (mtm-85) REVERT: B 91 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 156 LYS cc_start: 0.8915 (mttt) cc_final: 0.8428 (mtmt) REVERT: B 161 ASP cc_start: 0.8724 (t0) cc_final: 0.8432 (t0) REVERT: B 311 ILE cc_start: 0.9130 (mt) cc_final: 0.8795 (mm) REVERT: C 59 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 94 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8600 (tp40) REVERT: C 130 ARG cc_start: 0.7419 (ptt-90) cc_final: 0.6544 (tpt170) REVERT: C 176 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 285 LYS cc_start: 0.8522 (pttt) cc_final: 0.8145 (ptmm) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.2525 time to fit residues: 54.8513 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 : 0.763 ------------------------------------------------------------------------------- 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 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 158 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 163 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096830 restraints weight = 10847.853| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.25 r_work: 0.2826 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3809 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= 0.334 Angle : 0.564 6.840 10537 Z= 0.299 Chirality : 0.043 0.136 1197 Planarity : 0.004 0.035 1293 Dihedral : 15.349 140.381 1323 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.24 % Allowed : 19.57 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.60 (0.28), residues: 921 helix: -0.04 (0.26), residues: 420 sheet: 1.41 (0.48), residues: 132 loop : -1.45 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 138 PHE 0.018 0.002 PHE B 129 TYR 0.014 0.001 TYR B 315 ARG 0.005 0.000 ARG C 254 *********************** 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 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.841 Fit side-chains REVERT: A 247 ARG cc_start: 0.9010 (mtp85) cc_final: 0.8524 (mtm-85) REVERT: B 91 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 156 LYS cc_start: 0.8982 (mttt) cc_final: 0.8484 (mtmt) REVERT: C 59 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 130 ARG cc_start: 0.7718 (ptt-90) cc_final: 0.6593 (tpt170) REVERT: C 176 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 285 LYS cc_start: 0.8588 (pttt) cc_final: 0.8203 (ptmm) outliers start: 24 outliers final: 19 residues processed: 147 average time/residue: 0.2568 time to fit residues: 47.8551 Evaluate side-chains 150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 A residue 332 ASP 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 131 THR Chi-restraints excluded: chain B residue 163 GLU 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 174 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 216 TYR 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: 3.9990 chunk 92 optimal weight: 8.9990 chunk 50 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 40 optimal weight: 0.0020 chunk 85 optimal weight: 0.9980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098984 restraints weight = 10900.375| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.29 r_work: 0.2851 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7741 Z= 0.192 Angle : 0.494 5.343 10537 Z= 0.264 Chirality : 0.040 0.129 1197 Planarity : 0.003 0.023 1293 Dihedral : 15.100 143.014 1323 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.56 % Allowed : 20.11 % Favored : 77.33 % 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: -0.40 (0.28), residues: 921 helix: 0.23 (0.27), residues: 417 sheet: 1.09 (0.47), residues: 138 loop : -1.34 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 138 PHE 0.009 0.001 PHE B 129 TYR 0.007 0.001 TYR B 315 ARG 0.007 0.000 ARG C 254 *********************** 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 170 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.798 Fit side-chains REVERT: A 27 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8203 (ttm110) REVERT: A 205 TYR cc_start: 0.8649 (m-10) cc_final: 0.8328 (m-10) REVERT: A 206 GLN cc_start: 0.8937 (mt0) cc_final: 0.8647 (tt0) REVERT: A 247 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8547 (mtm-85) REVERT: B 91 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 156 LYS cc_start: 0.8908 (mttt) cc_final: 0.8418 (mtmt) REVERT: B 311 ILE cc_start: 0.9107 (mt) cc_final: 0.8754 (mm) REVERT: C 59 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 130 ARG cc_start: 0.7558 (ptt-90) cc_final: 0.6596 (tpt170) outliers start: 19 outliers final: 15 residues processed: 163 average time/residue: 0.2451 time to fit residues: 51.1245 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 255 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 185 VAL 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: 4.9990 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099715 restraints weight = 11009.853| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.30 r_work: 0.2861 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7741 Z= 0.182 Angle : 0.489 5.392 10537 Z= 0.262 Chirality : 0.040 0.126 1197 Planarity : 0.003 0.026 1293 Dihedral : 14.991 143.277 1323 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.56 % Allowed : 20.11 % Favored : 77.33 % 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: -0.32 (0.28), residues: 921 helix: 0.26 (0.27), residues: 426 sheet: 0.89 (0.47), residues: 141 loop : -1.19 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 199 PHE 0.010 0.001 PHE B 129 TYR 0.007 0.001 TYR B 315 ARG 0.007 0.000 ARG C 254 *********************** 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 171 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.791 Fit side-chains REVERT: A 205 TYR cc_start: 0.8649 (m-10) cc_final: 0.8226 (m-10) REVERT: A 206 GLN cc_start: 0.8941 (mt0) cc_final: 0.8679 (tt0) REVERT: A 247 ARG cc_start: 0.9044 (mtp85) cc_final: 0.8539 (mtm-85) REVERT: B 91 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8104 (tm-30) REVERT: B 156 LYS cc_start: 0.8942 (mttt) cc_final: 0.8464 (mtmt) REVERT: B 311 ILE cc_start: 0.9099 (mt) cc_final: 0.8748 (mm) REVERT: C 23 GLN cc_start: 0.7791 (mp10) cc_final: 0.7538 (mp10) REVERT: C 59 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 94 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8570 (tp40) REVERT: C 130 ARG cc_start: 0.7496 (ptt-90) cc_final: 0.6594 (tpt170) outliers start: 19 outliers final: 16 residues processed: 164 average time/residue: 0.2347 time to fit residues: 49.6192 Evaluate side-chains 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 163 GLU 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 63 ILE Chi-restraints excluded: chain C residue 185 VAL 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: 2.9990 chunk 75 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.123911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096301 restraints weight = 10852.717| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.39 r_work: 0.2814 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7741 Z= 0.283 Angle : 0.545 5.903 10537 Z= 0.290 Chirality : 0.042 0.136 1197 Planarity : 0.003 0.056 1293 Dihedral : 15.156 140.056 1323 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 20.65 % Favored : 77.19 % 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: -0.40 (0.28), residues: 921 helix: 0.22 (0.27), residues: 420 sheet: 0.93 (0.48), residues: 141 loop : -1.27 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 199 PHE 0.015 0.002 PHE B 129 TYR 0.012 0.001 TYR B 315 ARG 0.013 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 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.915 Fit side-chains REVERT: A 247 ARG cc_start: 0.9035 (mtp85) cc_final: 0.8514 (mtm-85) REVERT: B 91 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8082 (tm-30) REVERT: B 156 LYS cc_start: 0.8937 (mttt) cc_final: 0.8423 (mtmt) REVERT: B 222 ASP cc_start: 0.8567 (t0) cc_final: 0.8232 (m-30) REVERT: C 59 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 130 ARG cc_start: 0.7595 (ptt-90) cc_final: 0.6613 (tpt170) outliers start: 16 outliers final: 15 residues processed: 152 average time/residue: 0.2516 time to fit residues: 50.1442 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 : 0.963 ------------------------------------------------------------------------------- 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 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 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 185 VAL 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 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 0.0010 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.127221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100705 restraints weight = 10725.928| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.28 r_work: 0.2874 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7741 Z= 0.163 Angle : 0.486 5.361 10537 Z= 0.260 Chirality : 0.040 0.127 1197 Planarity : 0.003 0.049 1293 Dihedral : 14.905 142.484 1323 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.02 % Allowed : 20.92 % Favored : 77.06 % 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: -0.23 (0.28), residues: 921 helix: 0.37 (0.27), residues: 426 sheet: 0.90 (0.48), residues: 141 loop : -1.18 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 138 PHE 0.008 0.001 PHE B 129 TYR 0.004 0.001 TYR A 232 ARG 0.012 0.000 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.20 seconds wall clock time: 73 minutes 14.63 seconds (4394.63 seconds total)