Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 01:48:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/04_2023/6qcy_4513.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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 K 2 8.98 5 S 44 5.16 5 C 6936 2.51 5 N 1820 2.21 5 O 1844 1.98 5 H 11100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "D" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5436 Classifications: {'peptide': 355} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 333} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.73, per 1000 atoms: 0.45 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 100.1, 94.9, 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) K 2 19.00 S 44 16.00 O 1844 8.00 N 1820 7.00 C 6936 6.00 H 11100 1.00 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 - 3.50 Amino acid : False - 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: 16.74 Conformation dependent library (CDL) restraints added in 2.1 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 62.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.740A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.783A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.520A pdb=" N LEU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.624A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.804A pdb=" N ALA A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 104 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.741A pdb=" N LEU B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 29' Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.783A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.521A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 3.624A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP B 104 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 149 removed outlier: 4.130A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.962A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.739A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 24 " --> pdb=" O PRO C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 29' Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.783A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.521A pdb=" N LEU C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.624A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP C 104 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.740A pdb=" N LEU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.511A pdb=" N LEU D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.783A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.521A pdb=" N LEU D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 3.625A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.803A pdb=" N ALA D 102 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP D 104 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.367A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 149 removed outlier: 4.131A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.618A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 194 through 225 removed outlier: 3.645A pdb=" N GLY D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.963A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 334 through 352 removed outlier: 3.849A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 339 " --> pdb=" O PRO D 335 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 273 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 296 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU A 277 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL A 311 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR A 310 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 283 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 273 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 296 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU B 277 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 263 removed outlier: 6.566A pdb=" N VAL B 311 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 310 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 283 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 273 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 296 " --> pdb=" O PHE C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU C 277 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL C 311 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 310 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 283 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 273 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 296 " --> pdb=" O PHE D 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 254 through 256 removed outlier: 3.976A pdb=" N GLU D 277 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 263 removed outlier: 6.567A pdb=" N VAL D 311 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR D 310 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 283 " --> pdb=" O THR D 310 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 17.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 11088 1.02 - 1.22: 12 1.22 - 1.42: 4357 1.42 - 1.61: 6447 1.61 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" CA SER D 112 " pdb=" CB SER D 112 " ideal model delta sigma weight residual 1.528 1.464 0.064 2.61e-02 1.47e+03 6.00e+00 bond pdb=" CA SER A 112 " pdb=" CB SER A 112 " ideal model delta sigma weight residual 1.528 1.465 0.063 2.61e-02 1.47e+03 5.92e+00 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.528 1.466 0.063 2.61e-02 1.47e+03 5.78e+00 bond pdb=" CA SER C 112 " pdb=" CB SER C 112 " ideal model delta sigma weight residual 1.528 1.466 0.063 2.61e-02 1.47e+03 5.78e+00 bond pdb=" CB PHE A 214 " pdb=" CG PHE A 214 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.37e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.48: 415 105.48 - 112.69: 25948 112.69 - 119.90: 6145 119.90 - 127.11: 7272 127.11 - 134.31: 160 Bond angle restraints: 39940 Sorted by residual: angle pdb=" C LEU C 83 " pdb=" N VAL C 84 " pdb=" CA VAL C 84 " ideal model delta sigma weight residual 120.24 122.39 -2.15 6.30e-01 2.52e+00 1.17e+01 angle pdb=" C LEU B 83 " pdb=" N VAL B 84 " pdb=" CA VAL B 84 " ideal model delta sigma weight residual 120.24 122.36 -2.12 6.30e-01 2.52e+00 1.13e+01 angle pdb=" C LEU A 83 " pdb=" N VAL A 84 " pdb=" CA VAL A 84 " ideal model delta sigma weight residual 120.24 122.35 -2.11 6.30e-01 2.52e+00 1.12e+01 angle pdb=" C LEU D 83 " pdb=" N VAL D 84 " pdb=" CA VAL D 84 " ideal model delta sigma weight residual 120.24 122.34 -2.10 6.30e-01 2.52e+00 1.12e+01 angle pdb=" C SER D 324 " pdb=" N ALA D 325 " pdb=" CA ALA D 325 " ideal model delta sigma weight residual 120.82 125.47 -4.65 1.50e+00 4.44e-01 9.62e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 7981 14.78 - 29.55: 603 29.55 - 44.33: 72 44.33 - 59.10: 16 59.10 - 73.88: 12 Dihedral angle restraints: 8684 sinusoidal: 4000 harmonic: 4684 Sorted by residual: dihedral pdb=" CA ASN C 226 " pdb=" C ASN C 226 " pdb=" N TRP C 227 " pdb=" CA TRP C 227 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASN B 226 " pdb=" C ASN B 226 " pdb=" N TRP B 227 " pdb=" CA TRP B 227 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASN D 226 " pdb=" C ASN D 226 " pdb=" N TRP D 227 " pdb=" CA TRP D 227 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 906 0.030 - 0.061: 484 0.061 - 0.091: 261 0.091 - 0.121: 105 0.121 - 0.151: 28 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CA VAL A 68 " pdb=" N VAL A 68 " pdb=" C VAL A 68 " pdb=" CB VAL A 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA VAL D 68 " pdb=" N VAL D 68 " pdb=" C VAL D 68 " pdb=" CB VAL D 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA VAL C 68 " pdb=" N VAL C 68 " pdb=" C VAL C 68 " pdb=" CB VAL C 68 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 324 " 0.014 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" N ALA A 325 " -0.044 2.00e-02 2.50e+03 pdb=" CA ALA A 325 " 0.011 2.00e-02 2.50e+03 pdb=" H ALA A 325 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 49 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C TRP A 49 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 49 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 50 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 49 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C TRP D 49 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP D 49 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY D 50 " -0.013 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.36: 8074 2.36 - 3.05: 63885 3.05 - 3.75: 73394 3.75 - 4.44: 115439 4.44 - 5.14: 173136 Nonbonded interactions: 433928 Sorted by model distance: nonbonded pdb=" O LYS C 74 " pdb=" HE ARG C 110 " model vdw 1.660 1.850 nonbonded pdb=" O LYS B 74 " pdb=" HE ARG B 110 " model vdw 1.660 1.850 nonbonded pdb="HH11 ARG D 120 " pdb=" OE2 GLU D 217 " model vdw 1.660 1.850 nonbonded pdb=" O LYS A 74 " pdb=" HE ARG A 110 " model vdw 1.661 1.850 nonbonded pdb="HH11 ARG C 120 " pdb=" OE2 GLU C 217 " model vdw 1.661 1.850 ... (remaining 433923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 355) selection = chain 'C' selection = (chain 'D' and resid 1 through 355) } 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 group one per residue 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: 0.060 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: 0.330 Extract box with map and model: 2.280 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 68.810 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 : 0.009 0.064 10880 Z= 0.597 Angle : 1.045 7.547 14852 Z= 0.586 Chirality : 0.049 0.151 1784 Planarity : 0.007 0.048 1872 Dihedral : 9.698 73.880 3844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % Rotamer Outliers : 0.00 % 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: -4.43 (0.21), residues: 1412 helix: -3.94 (0.14), residues: 612 sheet: -4.03 (0.35), residues: 64 loop : -1.82 (0.25), residues: 736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.5096 time to fit residues: 250.2909 Evaluate side-chains 252 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN C 216 GLN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10880 Z= 0.212 Angle : 0.710 8.125 14852 Z= 0.379 Chirality : 0.041 0.155 1784 Planarity : 0.006 0.045 1872 Dihedral : 6.446 24.348 1536 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 0.00 % 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: -3.75 (0.22), residues: 1412 helix: -2.85 (0.16), residues: 704 sheet: -3.66 (0.43), residues: 64 loop : -1.74 (0.28), residues: 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5140 time to fit residues: 240.8159 Evaluate side-chains 262 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 137 optimal weight: 5.9990 chunk 113 optimal weight: 0.2980 chunk 126 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 30.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10880 Z= 0.188 Angle : 0.610 8.023 14852 Z= 0.328 Chirality : 0.039 0.144 1784 Planarity : 0.005 0.040 1872 Dihedral : 5.724 23.523 1536 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.00 % 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: -3.34 (0.21), residues: 1412 helix: -2.24 (0.17), residues: 732 sheet: -3.27 (0.52), residues: 64 loop : -1.88 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.5131 time to fit residues: 243.8313 Evaluate side-chains 280 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10880 Z= 0.193 Angle : 0.587 5.973 14852 Z= 0.313 Chirality : 0.038 0.133 1784 Planarity : 0.005 0.064 1872 Dihedral : 5.402 21.973 1536 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 0.00 % 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: -2.81 (0.22), residues: 1412 helix: -1.68 (0.18), residues: 716 sheet: -2.78 (0.61), residues: 64 loop : -1.86 (0.27), residues: 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.5256 time to fit residues: 237.4121 Evaluate side-chains 287 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10880 Z= 0.219 Angle : 0.602 5.920 14852 Z= 0.324 Chirality : 0.038 0.142 1784 Planarity : 0.005 0.044 1872 Dihedral : 5.293 21.114 1536 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer Outliers : 0.00 % 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: -2.80 (0.22), residues: 1412 helix: -1.61 (0.18), residues: 740 sheet: -2.77 (0.57), residues: 64 loop : -1.92 (0.27), residues: 608 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.5365 time to fit residues: 237.2242 Evaluate side-chains 276 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 40.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10880 Z= 0.271 Angle : 0.650 5.208 14852 Z= 0.352 Chirality : 0.038 0.125 1784 Planarity : 0.006 0.052 1872 Dihedral : 5.420 21.595 1536 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer Outliers : 0.00 % 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: -3.05 (0.21), residues: 1412 helix: -1.80 (0.18), residues: 744 sheet: -2.23 (0.63), residues: 64 loop : -2.15 (0.26), residues: 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.5589 time to fit residues: 254.0983 Evaluate side-chains 288 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 83 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10880 Z= 0.164 Angle : 0.558 5.354 14852 Z= 0.290 Chirality : 0.038 0.124 1784 Planarity : 0.004 0.040 1872 Dihedral : 5.067 21.241 1536 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.00 % 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: -2.61 (0.22), residues: 1412 helix: -1.36 (0.18), residues: 764 sheet: -2.25 (0.54), residues: 80 loop : -2.01 (0.27), residues: 568 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5209 time to fit residues: 225.4246 Evaluate side-chains 283 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10880 Z= 0.230 Angle : 0.611 5.233 14852 Z= 0.329 Chirality : 0.038 0.122 1784 Planarity : 0.005 0.052 1872 Dihedral : 5.131 21.450 1536 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer Outliers : 0.00 % 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: -2.92 (0.22), residues: 1412 helix: -1.54 (0.18), residues: 772 sheet: -2.28 (0.54), residues: 80 loop : -2.29 (0.27), residues: 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.5012 time to fit residues: 224.4506 Evaluate side-chains 276 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10880 Z= 0.175 Angle : 0.568 5.380 14852 Z= 0.297 Chirality : 0.038 0.131 1784 Planarity : 0.005 0.072 1872 Dihedral : 4.963 22.056 1536 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 0.00 % 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: -2.64 (0.22), residues: 1412 helix: -1.26 (0.18), residues: 768 sheet: -2.37 (0.55), residues: 80 loop : -2.22 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.5169 time to fit residues: 226.9361 Evaluate side-chains 294 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 40.0000 chunk 92 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 111 optimal weight: 0.0470 chunk 11 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 40.0000 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 10880 Z= 0.164 Angle : 0.557 5.134 14852 Z= 0.290 Chirality : 0.037 0.124 1784 Planarity : 0.005 0.070 1872 Dihedral : 4.746 21.247 1536 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 0.00 % 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: -2.44 (0.22), residues: 1412 helix: -1.03 (0.19), residues: 776 sheet: -2.50 (0.54), residues: 80 loop : -2.20 (0.27), residues: 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.5185 time to fit residues: 227.8015 Evaluate side-chains 291 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.221335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.183514 restraints weight = 70688.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189769 restraints weight = 38415.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194214 restraints weight = 24862.452| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 10880 Z= 0.146 Angle : 0.540 5.003 14852 Z= 0.278 Chirality : 0.037 0.122 1784 Planarity : 0.004 0.061 1872 Dihedral : 4.616 21.523 1536 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.00 % 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: -2.05 (0.23), residues: 1412 helix: -0.68 (0.19), residues: 772 sheet: -2.55 (0.52), residues: 80 loop : -2.04 (0.27), residues: 560 =============================================================================== Job complete usr+sys time: 4606.90 seconds wall clock time: 82 minutes 8.11 seconds (4928.11 seconds total)