Starting phenix.real_space_refine on Mon Mar 18 17:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/03_2024/6qcy_4513.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/03_2024/6qcy_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_4513/03_2024/6qcy_4513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/03_2024/6qcy_4513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/03_2024/6qcy_4513.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcy_4513/03_2024/6qcy_4513.pdb" } resolution = 4.7 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= 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.49, per 1000 atoms: 0.44 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: 16.73 Conformation dependent library (CDL) restraints added in 2.2 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: 1.83 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: 7.71 Time building geometry restraints manager: 17.64 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: 9233 14.78 - 29.55: 699 29.55 - 44.33: 220 44.33 - 59.10: 120 59.10 - 73.88: 16 Dihedral angle restraints: 10288 sinusoidal: 5604 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 10285 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 1.750 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 70.160 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.580 ------------------------------------------------------------------------------- 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 % Allowed : 1.47 % Favored : 98.53 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 104 HIS 0.005 0.003 HIS A 323 PHE 0.022 0.004 PHE A 236 TYR 0.023 0.004 TYR B 178 ARG 0.009 0.001 ARG A 63 *********************** 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 : 1.689 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: A 105 LEU cc_start: 0.9162 (mt) cc_final: 0.8761 (mt) REVERT: A 140 LEU cc_start: 0.8701 (tt) cc_final: 0.8442 (tp) REVERT: A 197 MET cc_start: 0.8472 (ttm) cc_final: 0.8195 (tpt) REVERT: A 317 VAL cc_start: 0.5414 (t) cc_final: 0.5149 (t) REVERT: B 140 LEU cc_start: 0.8799 (tt) cc_final: 0.8548 (tp) REVERT: B 317 VAL cc_start: 0.4860 (t) cc_final: 0.4655 (t) REVERT: C 52 TYR cc_start: 0.8372 (m-10) cc_final: 0.8154 (m-80) REVERT: C 140 LEU cc_start: 0.8714 (tt) cc_final: 0.8466 (tp) REVERT: C 317 VAL cc_start: 0.5035 (t) cc_final: 0.4734 (t) REVERT: D 140 LEU cc_start: 0.8835 (tt) cc_final: 0.8245 (tp) REVERT: D 197 MET cc_start: 0.8384 (ttm) cc_final: 0.8078 (tpp) REVERT: D 305 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6316 (pt0) REVERT: D 317 VAL cc_start: 0.5008 (t) cc_final: 0.4713 (t) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.4930 time to fit residues: 241.9662 Evaluate side-chains 256 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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: 6.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.6499 moved from start: 0.2734 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= 0.221 Angle : 0.708 7.774 14852 Z= 0.381 Chirality : 0.041 0.142 1784 Planarity : 0.006 0.049 1872 Dihedral : 6.551 24.675 1536 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -3.77 (0.22), residues: 1412 helix: -2.88 (0.16), residues: 704 sheet: -3.65 (0.44), residues: 64 loop : -1.73 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 167 HIS 0.003 0.001 HIS A 323 PHE 0.021 0.002 PHE A 114 TYR 0.011 0.002 TYR D 52 ARG 0.003 0.000 ARG D 220 *********************** 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 338 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.545 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.8157 (m-10) cc_final: 0.7951 (m-80) REVERT: A 105 LEU cc_start: 0.9133 (mt) cc_final: 0.8824 (mt) REVERT: A 197 MET cc_start: 0.8369 (ttm) cc_final: 0.7764 (tpp) REVERT: B 105 LEU cc_start: 0.9182 (mt) cc_final: 0.8912 (mt) REVERT: B 197 MET cc_start: 0.8359 (ttm) cc_final: 0.7737 (tpp) REVERT: C 52 TYR cc_start: 0.8060 (m-10) cc_final: 0.7730 (m-80) REVERT: C 105 LEU cc_start: 0.9214 (mt) cc_final: 0.8952 (mt) REVERT: C 197 MET cc_start: 0.8310 (ttm) cc_final: 0.7723 (tpp) REVERT: D 105 LEU cc_start: 0.9226 (mt) cc_final: 0.8923 (mt) REVERT: D 197 MET cc_start: 0.8306 (ttm) cc_final: 0.7826 (tpp) REVERT: D 305 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6224 (pt0) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.5105 time to fit residues: 241.0408 Evaluate side-chains 268 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 40.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 0.1980 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 overall best weight: 6.2390 ------------------------------------------------------------------------------- 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: 0.6546 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10880 Z= 0.214 Angle : 0.621 5.302 14852 Z= 0.340 Chirality : 0.039 0.124 1784 Planarity : 0.005 0.045 1872 Dihedral : 5.829 23.049 1536 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -3.50 (0.21), residues: 1412 helix: -2.32 (0.16), residues: 732 sheet: -3.40 (0.52), residues: 64 loop : -2.02 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 167 HIS 0.002 0.001 HIS B 323 PHE 0.022 0.002 PHE A 114 TYR 0.012 0.002 TYR B 215 ARG 0.005 0.000 ARG D 220 *********************** 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 336 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.675 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: A 101 CYS cc_start: 0.8167 (m) cc_final: 0.7898 (m) REVERT: A 105 LEU cc_start: 0.8997 (mt) cc_final: 0.8599 (mt) REVERT: A 197 MET cc_start: 0.8297 (ttm) cc_final: 0.7911 (tpp) REVERT: A 249 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8417 (mmt180) REVERT: B 101 CYS cc_start: 0.8203 (m) cc_final: 0.7992 (m) REVERT: B 105 LEU cc_start: 0.9104 (mt) cc_final: 0.8727 (mt) REVERT: B 197 MET cc_start: 0.8271 (ttm) cc_final: 0.7938 (tpp) REVERT: B 214 PHE cc_start: 0.8844 (t80) cc_final: 0.8626 (t80) REVERT: B 249 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.8561 (mmt180) REVERT: C 105 LEU cc_start: 0.9092 (mt) cc_final: 0.8688 (mt) REVERT: C 197 MET cc_start: 0.8204 (ttm) cc_final: 0.7742 (tpp) REVERT: C 249 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8495 (mmt180) REVERT: D 101 CYS cc_start: 0.8163 (m) cc_final: 0.7928 (m) REVERT: D 105 LEU cc_start: 0.9094 (mt) cc_final: 0.8702 (mt) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4939 time to fit residues: 232.2490 Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 7.9990 chunk 95 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10880 Z= 0.217 Angle : 0.593 7.151 14852 Z= 0.319 Chirality : 0.038 0.157 1784 Planarity : 0.005 0.066 1872 Dihedral : 5.476 21.031 1536 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -3.10 (0.22), residues: 1412 helix: -1.89 (0.17), residues: 740 sheet: -2.99 (0.58), residues: 64 loop : -2.01 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.002 0.001 HIS D 323 PHE 0.018 0.002 PHE A 114 TYR 0.010 0.002 TYR C 52 ARG 0.005 0.000 ARG B 254 *********************** 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 333 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.695 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: A 101 CYS cc_start: 0.8467 (m) cc_final: 0.8203 (m) REVERT: A 105 LEU cc_start: 0.9026 (mt) cc_final: 0.8580 (mt) REVERT: A 197 MET cc_start: 0.8410 (ttm) cc_final: 0.7977 (tpp) REVERT: A 246 GLU cc_start: 0.8393 (pt0) cc_final: 0.8147 (pm20) REVERT: B 101 CYS cc_start: 0.8391 (m) cc_final: 0.8184 (m) REVERT: B 105 LEU cc_start: 0.9141 (mt) cc_final: 0.8732 (mt) REVERT: B 197 MET cc_start: 0.8346 (ttm) cc_final: 0.7942 (tpp) REVERT: B 249 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8568 (mmm160) REVERT: C 101 CYS cc_start: 0.8629 (m) cc_final: 0.8380 (m) REVERT: C 105 LEU cc_start: 0.9150 (mt) cc_final: 0.8732 (mt) REVERT: C 197 MET cc_start: 0.8382 (ttm) cc_final: 0.7951 (tpp) REVERT: C 249 ARG cc_start: 0.8808 (mtt-85) cc_final: 0.8571 (mmm160) REVERT: D 105 LEU cc_start: 0.9104 (mt) cc_final: 0.8698 (mt) REVERT: D 197 MET cc_start: 0.8406 (ttm) cc_final: 0.7997 (tpp) REVERT: D 246 GLU cc_start: 0.8818 (pt0) cc_final: 0.8589 (mp0) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.5270 time to fit residues: 242.8553 Evaluate side-chains 295 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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: 10.0000 chunk 100 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- 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: 0.6613 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10880 Z= 0.212 Angle : 0.582 5.617 14852 Z= 0.313 Chirality : 0.038 0.157 1784 Planarity : 0.005 0.052 1872 Dihedral : 5.298 20.487 1536 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -2.74 (0.22), residues: 1412 helix: -1.56 (0.18), residues: 716 sheet: -2.86 (0.58), residues: 64 loop : -1.89 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 167 HIS 0.003 0.001 HIS C 323 PHE 0.014 0.001 PHE A 114 TYR 0.010 0.001 TYR B 10 ARG 0.006 0.000 ARG D 220 *********************** 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 323 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.835 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: A 101 CYS cc_start: 0.8608 (m) cc_final: 0.8316 (m) REVERT: A 105 LEU cc_start: 0.9073 (mt) cc_final: 0.8663 (mt) REVERT: A 127 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8292 (tpp80) REVERT: A 197 MET cc_start: 0.8220 (ttm) cc_final: 0.7921 (tpp) REVERT: B 164 GLN cc_start: 0.6657 (mp10) cc_final: 0.6397 (mp10) REVERT: B 197 MET cc_start: 0.8180 (ttm) cc_final: 0.7866 (tpp) REVERT: B 249 ARG cc_start: 0.8797 (mtt-85) cc_final: 0.8527 (mmm160) REVERT: C 164 GLN cc_start: 0.6782 (mp10) cc_final: 0.6482 (mp10) REVERT: C 197 MET cc_start: 0.8464 (ttm) cc_final: 0.7957 (tpp) REVERT: C 249 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8518 (mmm160) REVERT: D 246 GLU cc_start: 0.8746 (pt0) cc_final: 0.8540 (mp0) REVERT: D 305 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5616 (pt0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.5050 time to fit residues: 227.9290 Evaluate side-chains 277 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 135 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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: 0.6680 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10880 Z= 0.247 Angle : 0.612 4.950 14852 Z= 0.334 Chirality : 0.038 0.121 1784 Planarity : 0.005 0.049 1872 Dihedral : 5.307 21.012 1536 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -2.78 (0.22), residues: 1412 helix: -1.51 (0.19), residues: 716 sheet: -2.36 (0.66), residues: 64 loop : -2.08 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 104 HIS 0.002 0.001 HIS B 323 PHE 0.011 0.001 PHE A 114 TYR 0.017 0.002 TYR C 178 ARG 0.006 0.001 ARG A 220 *********************** 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 : 1.600 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: A 56 LEU cc_start: 0.9563 (tp) cc_final: 0.9363 (tp) REVERT: A 127 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8314 (tpp80) REVERT: C 127 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8366 (tpp80) REVERT: C 197 MET cc_start: 0.8428 (ttm) cc_final: 0.8195 (tpt) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.5456 time to fit residues: 249.5079 Evaluate side-chains 276 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 83 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 226 ASN B 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10880 Z= 0.178 Angle : 0.557 6.875 14852 Z= 0.294 Chirality : 0.038 0.139 1784 Planarity : 0.005 0.049 1872 Dihedral : 5.103 21.243 1536 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -2.53 (0.22), residues: 1412 helix: -1.22 (0.19), residues: 724 sheet: -2.27 (0.67), residues: 64 loop : -2.09 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 206 HIS 0.004 0.001 HIS B 323 PHE 0.010 0.001 PHE A 114 TYR 0.009 0.001 TYR C 178 ARG 0.005 0.000 ARG A 220 *********************** 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 315 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.682 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: A 56 LEU cc_start: 0.9551 (tp) cc_final: 0.9339 (tp) REVERT: A 127 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8376 (tpp80) REVERT: B 173 LEU cc_start: 0.8974 (tp) cc_final: 0.8772 (tt) REVERT: B 197 MET cc_start: 0.8743 (tpt) cc_final: 0.8477 (tpt) REVERT: B 214 PHE cc_start: 0.8532 (t80) cc_final: 0.8241 (t80) REVERT: C 56 LEU cc_start: 0.9529 (tp) cc_final: 0.9318 (tp) REVERT: C 127 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8382 (tpp80) REVERT: C 197 MET cc_start: 0.8598 (ttm) cc_final: 0.7997 (tpp) REVERT: D 305 GLU cc_start: 0.5907 (mt-10) cc_final: 0.5561 (pt0) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.5229 time to fit residues: 229.5108 Evaluate side-chains 296 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 chunk 12 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10880 Z= 0.180 Angle : 0.549 5.145 14852 Z= 0.292 Chirality : 0.037 0.117 1784 Planarity : 0.005 0.041 1872 Dihedral : 4.972 21.299 1536 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -2.49 (0.22), residues: 1412 helix: -1.10 (0.19), residues: 728 sheet: -2.36 (0.64), residues: 64 loop : -2.17 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.002 0.001 HIS C 323 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR B 178 ARG 0.012 0.000 ARG C 252 *********************** 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 316 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.630 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: A 56 LEU cc_start: 0.9501 (tp) cc_final: 0.9264 (tp) REVERT: A 127 ARG cc_start: 0.8601 (tpp80) cc_final: 0.8294 (tpp80) REVERT: B 56 LEU cc_start: 0.9528 (tp) cc_final: 0.9328 (tp) REVERT: B 173 LEU cc_start: 0.8964 (tp) cc_final: 0.8757 (tt) REVERT: B 197 MET cc_start: 0.8677 (tpt) cc_final: 0.8244 (tpt) REVERT: B 214 PHE cc_start: 0.8532 (t80) cc_final: 0.8260 (t80) REVERT: C 56 LEU cc_start: 0.9514 (tp) cc_final: 0.9293 (tp) REVERT: C 83 LEU cc_start: 0.8952 (mt) cc_final: 0.8716 (mt) REVERT: C 127 ARG cc_start: 0.8647 (tpp80) cc_final: 0.8369 (tpp80) REVERT: C 197 MET cc_start: 0.8318 (ttm) cc_final: 0.8046 (mmm) REVERT: D 197 MET cc_start: 0.8517 (ttm) cc_final: 0.8285 (tpt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.5162 time to fit residues: 225.2571 Evaluate side-chains 288 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10880 Z= 0.150 Angle : 0.519 4.959 14852 Z= 0.273 Chirality : 0.037 0.120 1784 Planarity : 0.005 0.074 1872 Dihedral : 4.761 20.971 1536 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.95 (0.23), residues: 1412 helix: -0.61 (0.20), residues: 688 sheet: -2.41 (0.63), residues: 64 loop : -1.88 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.002 0.001 HIS B 323 PHE 0.009 0.001 PHE A 341 TYR 0.006 0.001 TYR D 52 ARG 0.011 0.000 ARG A 110 *********************** 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 304 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.622 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: A 56 LEU cc_start: 0.9533 (tp) cc_final: 0.9275 (tp) REVERT: A 127 ARG cc_start: 0.8576 (tpp80) cc_final: 0.8290 (tpp80) REVERT: B 56 LEU cc_start: 0.9514 (tp) cc_final: 0.9308 (tp) REVERT: B 173 LEU cc_start: 0.8930 (tp) cc_final: 0.8728 (tt) REVERT: B 197 MET cc_start: 0.8724 (tpt) cc_final: 0.8381 (tpt) REVERT: C 56 LEU cc_start: 0.9503 (tp) cc_final: 0.9270 (tp) REVERT: C 83 LEU cc_start: 0.8930 (mt) cc_final: 0.8678 (mt) REVERT: C 127 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8336 (tpp80) REVERT: D 52 TYR cc_start: 0.8496 (m-80) cc_final: 0.8135 (m-80) REVERT: D 197 MET cc_start: 0.8555 (ttm) cc_final: 0.8312 (tpt) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.5069 time to fit residues: 214.1159 Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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: 0.0970 chunk 63 optimal weight: 40.0000 chunk 92 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 0.0370 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 0.0270 chunk 118 optimal weight: 10.0000 overall best weight: 1.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10880 Z= 0.140 Angle : 0.507 4.875 14852 Z= 0.263 Chirality : 0.037 0.120 1784 Planarity : 0.004 0.065 1872 Dihedral : 4.531 20.291 1536 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.58 (0.23), residues: 1412 helix: -0.23 (0.20), residues: 700 sheet: -2.48 (0.61), residues: 64 loop : -1.78 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 206 HIS 0.002 0.001 HIS D 323 PHE 0.012 0.001 PHE A 214 TYR 0.006 0.001 TYR A 215 ARG 0.011 0.000 ARG C 254 ********************** 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 297 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.560 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: A 56 LEU cc_start: 0.9530 (tp) cc_final: 0.9269 (tp) REVERT: A 83 LEU cc_start: 0.9014 (mt) cc_final: 0.8809 (mt) REVERT: A 127 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8265 (tpp80) REVERT: A 326 ASP cc_start: 0.9029 (m-30) cc_final: 0.8797 (m-30) REVERT: B 45 LEU cc_start: 0.8666 (mt) cc_final: 0.8415 (mt) REVERT: B 56 LEU cc_start: 0.9524 (tp) cc_final: 0.9311 (tp) REVERT: B 197 MET cc_start: 0.8738 (tpt) cc_final: 0.8372 (tpt) REVERT: C 56 LEU cc_start: 0.9520 (tp) cc_final: 0.9288 (tp) REVERT: C 83 LEU cc_start: 0.8923 (mt) cc_final: 0.8669 (mt) REVERT: C 127 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8172 (tpp80) REVERT: D 52 TYR cc_start: 0.8492 (m-80) cc_final: 0.8146 (m-80) REVERT: D 197 MET cc_start: 0.8600 (ttm) cc_final: 0.8354 (tpt) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.5184 time to fit residues: 213.2955 Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 0.0040 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** 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 = 0.4630 r_free = 0.4630 target = 0.223794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.186428 restraints weight = 69804.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192789 restraints weight = 37564.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.197325 restraints weight = 24225.664| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10880 Z= 0.133 Angle : 0.502 4.993 14852 Z= 0.259 Chirality : 0.037 0.120 1784 Planarity : 0.004 0.061 1872 Dihedral : 4.408 20.945 1536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.34 (0.23), residues: 1412 helix: 0.02 (0.21), residues: 704 sheet: -2.64 (0.58), residues: 64 loop : -1.71 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 206 HIS 0.003 0.001 HIS A 323 PHE 0.011 0.001 PHE D 341 TYR 0.005 0.001 TYR C 10 ARG 0.010 0.000 ARG C 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4815.98 seconds wall clock time: 85 minutes 13.22 seconds (5113.22 seconds total)