Starting phenix.real_space_refine on Mon Mar 18 17:33:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcz_4514/03_2024/6qcz_4514.pdb" } resolution = 4.4 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: "A" 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: 8.79, per 1000 atoms: 0.40 Number of scatterers: 21746 At special positions: 0 Unit cell: (102.7, 102.7, 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: 16.02 Conformation dependent library (CDL) restraints added in 2.1 seconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 65.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE A 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 3.576A pdb=" N ARG A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 4.027A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 105 through 111 removed outlier: 4.222A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.614A pdb=" N ALA A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (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 354 removed outlier: 3.901A pdb=" N ALA A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 92 removed outlier: 4.556A pdb=" N ILE B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Proline residue: B 85 - end of helix removed outlier: 4.027A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.223A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 247 " --> pdb=" O VAL B 243 " (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 354 removed outlier: 3.899A pdb=" N ALA B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.596A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 4.027A pdb=" N LEU C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 101 Processing helix chain 'C' and resid 105 through 111 removed outlier: 4.222A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 225 removed outlier: 3.753A pdb=" N ARG C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 247 " --> pdb=" O VAL C 243 " (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 354 removed outlier: 3.901A pdb=" N ALA C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.597A pdb=" N ILE D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.577A pdb=" N ARG D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA D 42 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 removed outlier: 4.557A pdb=" N ILE D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 4.027A pdb=" N LEU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 105 through 111 removed outlier: 4.223A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 152 removed outlier: 3.509A pdb=" N LEU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 161 through 174 removed outlier: 3.613A pdb=" N ALA D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 225 removed outlier: 3.752A pdb=" N ARG D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 4.129A pdb=" N LEU D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 247 " --> pdb=" O VAL D 243 " (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 354 removed outlier: 3.900A pdb=" N ALA D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 256 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA4, first strand: chain 'B' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA8, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AA9, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'D' and resid 253 through 256 Processing sheet with id=AB2, first strand: chain 'D' and resid 261 through 263 Processing sheet with id=AB3, first strand: chain 'D' and resid 294 through 296 520 hydrogen bonds defined for protein. 1416 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: 7.27 Time building geometry restraints manager: 16.80 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: 16 1.22 - 1.42: 4369 1.42 - 1.62: 6431 1.62 - 1.81: 76 Bond restraints: 21980 Sorted by residual: bond pdb=" N GLU D 305 " pdb=" CA GLU D 305 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.41e-02 5.03e+03 5.03e+00 bond pdb=" N GLU A 305 " pdb=" CA GLU A 305 " ideal model delta sigma weight residual 1.457 1.425 0.031 1.41e-02 5.03e+03 4.96e+00 bond pdb=" N GLU C 305 " pdb=" CA GLU C 305 " ideal model delta sigma weight residual 1.457 1.426 0.031 1.41e-02 5.03e+03 4.79e+00 bond pdb=" N GLU B 305 " pdb=" CA GLU B 305 " ideal model delta sigma weight residual 1.457 1.426 0.031 1.41e-02 5.03e+03 4.71e+00 bond pdb=" CG1 ILE D 30 " pdb=" CD1 ILE D 30 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 4.03e+00 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.37: 256 104.37 - 111.83: 25274 111.83 - 119.29: 5800 119.29 - 126.75: 8423 126.75 - 134.21: 187 Bond angle restraints: 39940 Sorted by residual: angle pdb=" N ASN D 124 " pdb=" CA ASN D 124 " pdb=" C ASN D 124 " ideal model delta sigma weight residual 114.04 109.21 4.83 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N ASN C 124 " pdb=" CA ASN C 124 " pdb=" C ASN C 124 " ideal model delta sigma weight residual 114.04 109.22 4.82 1.24e+00 6.50e-01 1.51e+01 angle pdb=" N ASN B 124 " pdb=" CA ASN B 124 " pdb=" C ASN B 124 " ideal model delta sigma weight residual 114.04 109.24 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" N ASN A 124 " pdb=" CA ASN A 124 " pdb=" C ASN A 124 " ideal model delta sigma weight residual 114.04 109.25 4.79 1.24e+00 6.50e-01 1.49e+01 angle pdb=" N ALA A 294 " pdb=" CA ALA A 294 " pdb=" C ALA A 294 " ideal model delta sigma weight residual 108.86 113.28 -4.42 1.41e+00 5.03e-01 9.83e+00 ... (remaining 39935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 9280 14.92 - 29.83: 685 29.83 - 44.75: 199 44.75 - 59.67: 116 59.67 - 74.59: 8 Dihedral angle restraints: 10288 sinusoidal: 5604 harmonic: 4684 Sorted by residual: dihedral pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N ALA A 26 " pdb=" CA ALA A 26 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL C 25 " pdb=" C VAL C 25 " pdb=" N ALA C 26 " pdb=" CA ALA C 26 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA VAL D 25 " pdb=" C VAL D 25 " pdb=" N ALA D 26 " pdb=" CA ALA D 26 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 10285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 957 0.031 - 0.062: 496 0.062 - 0.093: 219 0.093 - 0.124: 92 0.124 - 0.156: 20 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CG LEU C 106 " pdb=" CB LEU C 106 " pdb=" CD1 LEU C 106 " pdb=" CD2 LEU C 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CG LEU D 106 " pdb=" CB LEU D 106 " pdb=" CD1 LEU D 106 " pdb=" CD2 LEU D 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 1781 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 176 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C THR D 176 " -0.034 2.00e-02 2.50e+03 pdb=" O THR D 176 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY D 177 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 176 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C THR A 176 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A 176 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 177 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 176 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C THR C 176 " 0.033 2.00e-02 2.50e+03 pdb=" O THR C 176 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 177 " -0.011 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.32: 5967 2.32 - 3.03: 62504 3.03 - 3.73: 74299 3.73 - 4.44: 114856 4.44 - 5.14: 175144 Nonbonded interactions: 432770 Sorted by model distance: nonbonded pdb=" O LYS D 74 " pdb=" HE ARG D 110 " model vdw 1.618 1.850 nonbonded pdb=" O LYS A 74 " pdb=" HE ARG A 110 " model vdw 1.618 1.850 nonbonded pdb=" O LYS C 74 " pdb=" HE ARG C 110 " model vdw 1.619 1.850 nonbonded pdb=" O LYS B 74 " pdb=" HE ARG B 110 " model vdw 1.619 1.850 nonbonded pdb=" H GLY A 259 " pdb=" O ALA A 313 " model vdw 1.651 1.850 ... (remaining 432765 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' and resid 1 through 355) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 355) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.320 Extract box with map and model: 1.590 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 67.380 Find NCS groups from input model: 0.990 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 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 0.078 10880 Z= 0.598 Angle : 1.002 7.056 14852 Z= 0.558 Chirality : 0.048 0.156 1784 Planarity : 0.006 0.039 1872 Dihedral : 9.452 74.586 3844 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % 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: -4.17 (0.21), residues: 1412 helix: -3.45 (0.15), residues: 592 sheet: -3.55 (0.60), residues: 40 loop : -2.13 (0.25), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 227 HIS 0.005 0.003 HIS B 323 PHE 0.018 0.003 PHE D 141 TYR 0.023 0.005 TYR C 178 ARG 0.010 0.002 ARG C 220 *********************** 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 455 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 1.615 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: A 155 GLN cc_start: 0.8133 (mt0) cc_final: 0.7873 (mt0) REVERT: A 247 ILE cc_start: 0.8980 (mt) cc_final: 0.8668 (tp) REVERT: A 272 MET cc_start: 0.6080 (ptm) cc_final: 0.5817 (ptm) REVERT: A 327 PHE cc_start: 0.7039 (t80) cc_final: 0.6571 (t80) REVERT: A 346 LEU cc_start: 0.8351 (mt) cc_final: 0.8142 (tt) REVERT: B 155 GLN cc_start: 0.8144 (mt0) cc_final: 0.7848 (mt0) REVERT: B 327 PHE cc_start: 0.7138 (t80) cc_final: 0.6650 (t80) REVERT: B 346 LEU cc_start: 0.8372 (mt) cc_final: 0.8115 (tt) REVERT: C 155 GLN cc_start: 0.7830 (mt0) cc_final: 0.7531 (mt0) REVERT: C 247 ILE cc_start: 0.8905 (mt) cc_final: 0.8676 (tp) REVERT: C 327 PHE cc_start: 0.7141 (t80) cc_final: 0.6643 (t80) REVERT: C 346 LEU cc_start: 0.8369 (mt) cc_final: 0.8089 (tt) REVERT: D 155 GLN cc_start: 0.8100 (mt0) cc_final: 0.7688 (mt0) REVERT: D 247 ILE cc_start: 0.8967 (mt) cc_final: 0.8656 (tp) REVERT: D 327 PHE cc_start: 0.7136 (t80) cc_final: 0.6664 (t80) REVERT: D 346 LEU cc_start: 0.8277 (mt) cc_final: 0.7954 (tt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.5375 time to fit residues: 332.6433 Evaluate side-chains 346 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10880 Z= 0.272 Angle : 0.762 9.279 14852 Z= 0.408 Chirality : 0.042 0.147 1784 Planarity : 0.007 0.056 1872 Dihedral : 6.669 26.356 1536 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.09 % Allowed : 1.37 % 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: -3.96 (0.20), residues: 1412 helix: -2.83 (0.15), residues: 700 sheet: -2.73 (0.75), residues: 40 loop : -2.29 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 49 HIS 0.002 0.001 HIS A 323 PHE 0.025 0.002 PHE B 214 TYR 0.011 0.002 TYR A 148 ARG 0.009 0.001 ARG B 348 *********************** 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 382 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 1.618 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: A 78 ASP cc_start: 0.6900 (m-30) cc_final: 0.6639 (m-30) REVERT: A 155 GLN cc_start: 0.7949 (mt0) cc_final: 0.7632 (mt0) REVERT: A 272 MET cc_start: 0.5978 (ptm) cc_final: 0.5771 (ptm) REVERT: A 327 PHE cc_start: 0.6889 (t80) cc_final: 0.6615 (t80) REVERT: A 346 LEU cc_start: 0.8353 (mt) cc_final: 0.8036 (tt) REVERT: B 78 ASP cc_start: 0.6913 (m-30) cc_final: 0.6642 (m-30) REVERT: B 170 VAL cc_start: 0.8559 (m) cc_final: 0.8129 (p) REVERT: B 327 PHE cc_start: 0.7043 (t80) cc_final: 0.6619 (t80) REVERT: B 346 LEU cc_start: 0.8260 (mt) cc_final: 0.8024 (tt) REVERT: C 78 ASP cc_start: 0.6910 (m-30) cc_final: 0.6665 (m-30) REVERT: C 155 GLN cc_start: 0.7383 (mt0) cc_final: 0.7038 (mt0) REVERT: C 170 VAL cc_start: 0.8390 (m) cc_final: 0.7963 (p) REVERT: C 327 PHE cc_start: 0.7019 (t80) cc_final: 0.6616 (t80) REVERT: C 346 LEU cc_start: 0.8141 (mt) cc_final: 0.7896 (tt) REVERT: D 78 ASP cc_start: 0.6862 (m-30) cc_final: 0.6604 (m-30) REVERT: D 155 GLN cc_start: 0.7739 (mt0) cc_final: 0.7223 (mt0) REVERT: D 243 VAL cc_start: 0.9223 (t) cc_final: 0.8893 (t) REVERT: D 346 LEU cc_start: 0.8086 (mt) cc_final: 0.7785 (tt) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.4493 time to fit residues: 252.2655 Evaluate side-chains 328 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 127 optimal weight: 0.0970 chunk 137 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 chunk 102 optimal weight: 40.0000 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10880 Z= 0.196 Angle : 0.632 5.923 14852 Z= 0.338 Chirality : 0.040 0.144 1784 Planarity : 0.005 0.030 1872 Dihedral : 5.950 20.314 1536 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -3.52 (0.21), residues: 1412 helix: -2.13 (0.17), residues: 708 sheet: -2.91 (0.75), residues: 40 loop : -2.47 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.001 0.001 HIS B 323 PHE 0.017 0.001 PHE B 214 TYR 0.009 0.001 TYR A 10 ARG 0.019 0.001 ARG B 189 *********************** 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 391 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.566 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: A 78 ASP cc_start: 0.6676 (m-30) cc_final: 0.6340 (m-30) REVERT: A 155 GLN cc_start: 0.7661 (mt0) cc_final: 0.7154 (mt0) REVERT: A 164 GLN cc_start: 0.7136 (mp10) cc_final: 0.6931 (mp10) REVERT: A 272 MET cc_start: 0.5859 (ptm) cc_final: 0.5594 (ptm) REVERT: A 346 LEU cc_start: 0.8215 (mt) cc_final: 0.7974 (tt) REVERT: B 78 ASP cc_start: 0.6676 (m-30) cc_final: 0.6372 (m-30) REVERT: B 155 GLN cc_start: 0.7481 (mt0) cc_final: 0.7223 (mt0) REVERT: B 196 MET cc_start: 0.8476 (mpp) cc_final: 0.8230 (mpp) REVERT: B 206 TRP cc_start: 0.8216 (t60) cc_final: 0.7598 (t60) REVERT: B 228 GLN cc_start: 0.8733 (mt0) cc_final: 0.8470 (pt0) REVERT: B 247 ILE cc_start: 0.9053 (pt) cc_final: 0.8603 (tp) REVERT: B 346 LEU cc_start: 0.8105 (mt) cc_final: 0.7900 (tt) REVERT: C 78 ASP cc_start: 0.6659 (m-30) cc_final: 0.6383 (m-30) REVERT: C 155 GLN cc_start: 0.7606 (mt0) cc_final: 0.7017 (mt0) REVERT: C 164 GLN cc_start: 0.7210 (mp10) cc_final: 0.6940 (mp10) REVERT: C 217 GLU cc_start: 0.8271 (tp30) cc_final: 0.8000 (tp30) REVERT: C 346 LEU cc_start: 0.8156 (mt) cc_final: 0.7930 (tt) REVERT: D 78 ASP cc_start: 0.6783 (m-30) cc_final: 0.6443 (m-30) REVERT: D 155 GLN cc_start: 0.7659 (mt0) cc_final: 0.7169 (mt0) REVERT: D 164 GLN cc_start: 0.6949 (mp10) cc_final: 0.6693 (mp10) REVERT: D 346 LEU cc_start: 0.8166 (mt) cc_final: 0.7929 (tt) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.4259 time to fit residues: 244.2513 Evaluate side-chains 341 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 50.0000 chunk 121 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 overall best weight: 8.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10880 Z= 0.246 Angle : 0.653 5.731 14852 Z= 0.349 Chirality : 0.040 0.132 1784 Planarity : 0.005 0.061 1872 Dihedral : 5.699 20.536 1536 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -3.30 (0.21), residues: 1412 helix: -1.88 (0.17), residues: 732 sheet: -2.85 (0.57), residues: 64 loop : -2.39 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 168 HIS 0.002 0.001 HIS A 323 PHE 0.027 0.002 PHE B 214 TYR 0.010 0.002 TYR C 10 ARG 0.009 0.001 ARG B 189 *********************** 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 383 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.553 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: A 78 ASP cc_start: 0.7067 (m-30) cc_final: 0.6841 (m-30) REVERT: A 155 GLN cc_start: 0.7616 (mt0) cc_final: 0.7067 (mt0) REVERT: A 272 MET cc_start: 0.5873 (ptm) cc_final: 0.5245 (ptm) REVERT: A 346 LEU cc_start: 0.8367 (mt) cc_final: 0.8055 (tt) REVERT: B 78 ASP cc_start: 0.7094 (m-30) cc_final: 0.6873 (m-30) REVERT: B 247 ILE cc_start: 0.9041 (pt) cc_final: 0.8571 (tp) REVERT: B 307 ARG cc_start: 0.5664 (mmm160) cc_final: 0.5449 (mmm160) REVERT: B 346 LEU cc_start: 0.8224 (mt) cc_final: 0.8003 (tt) REVERT: C 78 ASP cc_start: 0.7089 (m-30) cc_final: 0.6868 (m-30) REVERT: C 155 GLN cc_start: 0.7648 (mt0) cc_final: 0.7122 (mt0) REVERT: C 217 GLU cc_start: 0.8111 (tp30) cc_final: 0.7881 (tp30) REVERT: C 346 LEU cc_start: 0.8301 (mt) cc_final: 0.8030 (tt) REVERT: D 78 ASP cc_start: 0.7023 (m-30) cc_final: 0.6801 (m-30) REVERT: D 155 GLN cc_start: 0.7622 (mt0) cc_final: 0.7251 (mt0) REVERT: D 206 TRP cc_start: 0.8094 (t60) cc_final: 0.7799 (t60) REVERT: D 346 LEU cc_start: 0.8202 (mt) cc_final: 0.7966 (tt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.4224 time to fit residues: 236.0056 Evaluate side-chains 334 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 0.2980 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 overall best weight: 6.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10880 Z= 0.199 Angle : 0.603 5.799 14852 Z= 0.318 Chirality : 0.039 0.123 1784 Planarity : 0.004 0.040 1872 Dihedral : 5.432 19.666 1536 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.99 (0.21), residues: 1412 helix: -1.62 (0.18), residues: 712 sheet: -2.87 (0.56), residues: 64 loop : -2.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.002 0.001 HIS D 323 PHE 0.046 0.002 PHE C 214 TYR 0.013 0.002 TYR C 178 ARG 0.004 0.000 ARG B 189 *********************** 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 372 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.734 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: A 78 ASP cc_start: 0.7141 (m-30) cc_final: 0.6920 (m-30) REVERT: A 155 GLN cc_start: 0.7525 (mt0) cc_final: 0.6986 (mt0) REVERT: A 346 LEU cc_start: 0.8364 (mt) cc_final: 0.7970 (tt) REVERT: B 78 ASP cc_start: 0.6869 (m-30) cc_final: 0.6600 (m-30) REVERT: B 247 ILE cc_start: 0.9033 (pt) cc_final: 0.8575 (tp) REVERT: B 307 ARG cc_start: 0.5690 (mmm160) cc_final: 0.5438 (mmm160) REVERT: B 346 LEU cc_start: 0.8237 (mt) cc_final: 0.7997 (tt) REVERT: C 59 THR cc_start: 0.7167 (p) cc_final: 0.6687 (p) REVERT: C 78 ASP cc_start: 0.6867 (m-30) cc_final: 0.6585 (m-30) REVERT: C 155 GLN cc_start: 0.7599 (mt0) cc_final: 0.6936 (mt0) REVERT: C 184 GLN cc_start: 0.7133 (mp10) cc_final: 0.6844 (mp10) REVERT: C 217 GLU cc_start: 0.8067 (tp30) cc_final: 0.7663 (tp30) REVERT: C 346 LEU cc_start: 0.8307 (mt) cc_final: 0.8035 (tt) REVERT: D 78 ASP cc_start: 0.7035 (m-30) cc_final: 0.6721 (m-30) REVERT: D 155 GLN cc_start: 0.7736 (mt0) cc_final: 0.7200 (mt0) REVERT: D 206 TRP cc_start: 0.8070 (t60) cc_final: 0.7819 (t60) REVERT: D 346 LEU cc_start: 0.8177 (mt) cc_final: 0.7971 (tt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.4338 time to fit residues: 237.8578 Evaluate side-chains 336 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 0.0970 overall best weight: 3.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10880 Z= 0.164 Angle : 0.580 6.536 14852 Z= 0.297 Chirality : 0.039 0.131 1784 Planarity : 0.004 0.041 1872 Dihedral : 5.094 19.569 1536 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -2.57 (0.22), residues: 1412 helix: -1.21 (0.19), residues: 720 sheet: -2.88 (0.73), residues: 40 loop : -2.15 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.004 0.002 HIS C 323 PHE 0.049 0.001 PHE B 214 TYR 0.008 0.001 TYR C 10 ARG 0.004 0.000 ARG B 189 *********************** 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 376 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.655 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: A 59 THR cc_start: 0.7098 (p) cc_final: 0.6791 (p) REVERT: A 78 ASP cc_start: 0.7324 (m-30) cc_final: 0.7081 (m-30) REVERT: A 155 GLN cc_start: 0.7494 (mt0) cc_final: 0.6939 (mt0) REVERT: A 346 LEU cc_start: 0.8325 (mt) cc_final: 0.8030 (tt) REVERT: B 1 MET cc_start: -0.4404 (ptt) cc_final: -0.4831 (ptt) REVERT: B 59 THR cc_start: 0.7199 (p) cc_final: 0.6857 (p) REVERT: B 78 ASP cc_start: 0.6894 (m-30) cc_final: 0.6621 (m-30) REVERT: B 184 GLN cc_start: 0.7858 (mt0) cc_final: 0.6946 (mp10) REVERT: B 189 ARG cc_start: 0.8340 (mmt90) cc_final: 0.8131 (mmt90) REVERT: B 247 ILE cc_start: 0.8993 (pt) cc_final: 0.8534 (tp) REVERT: B 346 LEU cc_start: 0.8238 (mt) cc_final: 0.7998 (tt) REVERT: C 59 THR cc_start: 0.7064 (p) cc_final: 0.6572 (p) REVERT: C 78 ASP cc_start: 0.7060 (m-30) cc_final: 0.6755 (m-30) REVERT: C 155 GLN cc_start: 0.7602 (mt0) cc_final: 0.6905 (mt0) REVERT: C 184 GLN cc_start: 0.7286 (mp10) cc_final: 0.6948 (mp10) REVERT: C 217 GLU cc_start: 0.7948 (tp30) cc_final: 0.7617 (tp30) REVERT: C 346 LEU cc_start: 0.8370 (mt) cc_final: 0.8055 (tt) REVERT: D 59 THR cc_start: 0.7199 (p) cc_final: 0.6689 (p) REVERT: D 78 ASP cc_start: 0.6701 (m-30) cc_final: 0.6333 (m-30) REVERT: D 155 GLN cc_start: 0.7682 (mt0) cc_final: 0.7162 (mt0) REVERT: D 217 GLU cc_start: 0.8162 (tp30) cc_final: 0.7714 (tp30) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.4198 time to fit residues: 231.6285 Evaluate side-chains 339 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 83 optimal weight: 3.9990 overall best weight: 7.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10880 Z= 0.234 Angle : 0.617 5.376 14852 Z= 0.327 Chirality : 0.040 0.155 1784 Planarity : 0.005 0.044 1872 Dihedral : 5.117 20.112 1536 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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: -2.71 (0.22), residues: 1412 helix: -1.37 (0.17), residues: 752 sheet: -2.96 (0.56), residues: 64 loop : -2.11 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.006 0.003 HIS D 323 PHE 0.045 0.002 PHE C 214 TYR 0.018 0.002 TYR C 178 ARG 0.005 0.000 ARG C 71 *********************** 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 367 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.373 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: A 78 ASP cc_start: 0.7067 (m-30) cc_final: 0.6865 (m-30) REVERT: A 155 GLN cc_start: 0.7463 (mt0) cc_final: 0.6821 (mt0) REVERT: A 189 ARG cc_start: 0.8291 (mtt180) cc_final: 0.8044 (mtt180) REVERT: A 346 LEU cc_start: 0.8337 (mt) cc_final: 0.8048 (tt) REVERT: B 59 THR cc_start: 0.7003 (p) cc_final: 0.6544 (p) REVERT: B 78 ASP cc_start: 0.7183 (m-30) cc_final: 0.6970 (m-30) REVERT: B 189 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8171 (mmt90) REVERT: B 247 ILE cc_start: 0.8957 (pt) cc_final: 0.8419 (tp) REVERT: B 346 LEU cc_start: 0.8260 (mt) cc_final: 0.8000 (tt) REVERT: C 155 GLN cc_start: 0.7670 (mt0) cc_final: 0.6919 (mt0) REVERT: C 184 GLN cc_start: 0.7178 (mp10) cc_final: 0.6952 (mp10) REVERT: C 217 GLU cc_start: 0.7843 (tp30) cc_final: 0.7584 (tp30) REVERT: C 346 LEU cc_start: 0.8389 (mt) cc_final: 0.8085 (tt) REVERT: D 155 GLN cc_start: 0.7718 (mt0) cc_final: 0.7171 (mt0) REVERT: D 217 GLU cc_start: 0.8220 (tp30) cc_final: 0.7947 (tp30) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.4210 time to fit residues: 225.3402 Evaluate side-chains 334 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 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: 3.9990 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10880 Z= 0.179 Angle : 0.578 5.426 14852 Z= 0.301 Chirality : 0.039 0.121 1784 Planarity : 0.004 0.045 1872 Dihedral : 4.928 19.282 1536 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % 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: -2.41 (0.22), residues: 1412 helix: -1.07 (0.18), residues: 752 sheet: -2.95 (0.57), residues: 64 loop : -2.03 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.003 0.002 HIS C 323 PHE 0.049 0.001 PHE B 214 TYR 0.009 0.002 TYR C 178 ARG 0.003 0.000 ARG A 71 *********************** 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 367 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.350 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: A 78 ASP cc_start: 0.7008 (m-30) cc_final: 0.6766 (m-30) REVERT: A 155 GLN cc_start: 0.7262 (mt0) cc_final: 0.6623 (mt0) REVERT: A 189 ARG cc_start: 0.8289 (mtt180) cc_final: 0.8047 (mtt180) REVERT: A 346 LEU cc_start: 0.8362 (mt) cc_final: 0.8105 (tt) REVERT: B 1 MET cc_start: -0.4635 (ptt) cc_final: -0.5137 (ptt) REVERT: B 33 MET cc_start: 0.5745 (mmm) cc_final: 0.5542 (mmm) REVERT: B 59 THR cc_start: 0.7177 (p) cc_final: 0.6789 (p) REVERT: B 78 ASP cc_start: 0.6844 (m-30) cc_final: 0.6640 (m-30) REVERT: B 155 GLN cc_start: 0.7397 (mt0) cc_final: 0.6340 (mt0) REVERT: B 184 GLN cc_start: 0.7942 (mt0) cc_final: 0.6886 (mp10) REVERT: B 189 ARG cc_start: 0.8336 (mmt90) cc_final: 0.8136 (mmt90) REVERT: B 247 ILE cc_start: 0.8946 (pt) cc_final: 0.8423 (tp) REVERT: B 346 LEU cc_start: 0.8250 (mt) cc_final: 0.7993 (tt) REVERT: C 78 ASP cc_start: 0.7318 (m-30) cc_final: 0.7028 (m-30) REVERT: C 155 GLN cc_start: 0.7603 (mt0) cc_final: 0.6811 (mt0) REVERT: C 184 GLN cc_start: 0.7163 (mp10) cc_final: 0.6944 (mp10) REVERT: C 189 ARG cc_start: 0.8332 (mtt180) cc_final: 0.8124 (mtt180) REVERT: C 217 GLU cc_start: 0.7881 (tp30) cc_final: 0.7670 (tp30) REVERT: C 346 LEU cc_start: 0.8377 (mt) cc_final: 0.8073 (tt) REVERT: D 155 GLN cc_start: 0.7634 (mt0) cc_final: 0.7073 (mt0) REVERT: D 217 GLU cc_start: 0.8158 (tp30) cc_final: 0.7707 (tp30) REVERT: D 225 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7596 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.4506 time to fit residues: 237.5336 Evaluate side-chains 332 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10880 Z= 0.201 Angle : 0.590 5.463 14852 Z= 0.309 Chirality : 0.039 0.122 1784 Planarity : 0.004 0.042 1872 Dihedral : 4.908 20.441 1536 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % 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: -2.41 (0.22), residues: 1412 helix: -1.05 (0.18), residues: 760 sheet: -3.06 (0.54), residues: 64 loop : -2.04 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 206 HIS 0.003 0.002 HIS B 323 PHE 0.029 0.001 PHE C 214 TYR 0.014 0.002 TYR C 178 ARG 0.004 0.000 ARG D 307 *********************** 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 371 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.732 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: A 59 THR cc_start: 0.7056 (p) cc_final: 0.6615 (p) REVERT: A 155 GLN cc_start: 0.7336 (mt0) cc_final: 0.6667 (mt0) REVERT: A 189 ARG cc_start: 0.8239 (mtt180) cc_final: 0.8022 (mtt180) REVERT: A 206 TRP cc_start: 0.8349 (t60) cc_final: 0.7934 (t60) REVERT: A 307 ARG cc_start: 0.5616 (mmm160) cc_final: 0.5163 (mmm160) REVERT: A 346 LEU cc_start: 0.8426 (mt) cc_final: 0.8179 (tt) REVERT: B 1 MET cc_start: -0.4481 (ptt) cc_final: -0.5048 (ptt) REVERT: B 33 MET cc_start: 0.5773 (mmm) cc_final: 0.5569 (mmm) REVERT: B 79 VAL cc_start: 0.9161 (t) cc_final: 0.8956 (t) REVERT: B 155 GLN cc_start: 0.7416 (mt0) cc_final: 0.6329 (mt0) REVERT: B 184 GLN cc_start: 0.7954 (mt0) cc_final: 0.6841 (mp10) REVERT: B 247 ILE cc_start: 0.8935 (pt) cc_final: 0.8409 (tp) REVERT: B 272 MET cc_start: 0.6077 (ptm) cc_final: 0.5737 (ptm) REVERT: C 155 GLN cc_start: 0.7599 (mt0) cc_final: 0.6796 (mt0) REVERT: C 184 GLN cc_start: 0.7139 (mp10) cc_final: 0.6918 (mp10) REVERT: C 220 ARG cc_start: 0.7997 (tpt-90) cc_final: 0.7520 (tpt-90) REVERT: C 346 LEU cc_start: 0.8386 (mt) cc_final: 0.8073 (tt) REVERT: D 79 VAL cc_start: 0.9079 (t) cc_final: 0.8873 (t) REVERT: D 141 PHE cc_start: 0.8138 (t80) cc_final: 0.7022 (t80) REVERT: D 155 GLN cc_start: 0.7648 (mt0) cc_final: 0.7037 (mt0) REVERT: D 217 GLU cc_start: 0.8282 (tp30) cc_final: 0.7724 (tp30) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.4473 time to fit residues: 239.0525 Evaluate side-chains 339 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10880 Z= 0.210 Angle : 0.599 5.499 14852 Z= 0.315 Chirality : 0.040 0.129 1784 Planarity : 0.004 0.043 1872 Dihedral : 4.903 19.995 1536 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % 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: -2.40 (0.22), residues: 1412 helix: -1.06 (0.18), residues: 760 sheet: -3.12 (0.54), residues: 64 loop : -2.00 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 206 HIS 0.005 0.002 HIS D 323 PHE 0.034 0.002 PHE B 214 TYR 0.015 0.002 TYR D 178 ARG 0.004 0.000 ARG A 219 ********************** 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 363 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.654 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: A 135 LEU cc_start: 0.9247 (tt) cc_final: 0.8698 (mp) REVERT: A 155 GLN cc_start: 0.7319 (mt0) cc_final: 0.6657 (mt0) REVERT: A 206 TRP cc_start: 0.8381 (t60) cc_final: 0.7898 (t60) REVERT: A 307 ARG cc_start: 0.5799 (mmm160) cc_final: 0.4815 (tpt170) REVERT: A 346 LEU cc_start: 0.8421 (mt) cc_final: 0.8176 (tt) REVERT: B 1 MET cc_start: -0.4477 (ptt) cc_final: -0.5095 (ptt) REVERT: B 155 GLN cc_start: 0.7448 (mt0) cc_final: 0.6427 (mt0) REVERT: B 184 GLN cc_start: 0.7890 (mt0) cc_final: 0.6792 (mp10) REVERT: B 247 ILE cc_start: 0.8896 (pt) cc_final: 0.8265 (tp) REVERT: C 135 LEU cc_start: 0.9275 (tt) cc_final: 0.8744 (mp) REVERT: C 155 GLN cc_start: 0.7581 (mt0) cc_final: 0.6780 (mt0) REVERT: C 184 GLN cc_start: 0.7110 (mp10) cc_final: 0.6901 (mp10) REVERT: C 346 LEU cc_start: 0.8448 (mt) cc_final: 0.8142 (tt) REVERT: D 135 LEU cc_start: 0.9133 (tt) cc_final: 0.8633 (mp) REVERT: D 141 PHE cc_start: 0.8231 (t80) cc_final: 0.7164 (t80) REVERT: D 155 GLN cc_start: 0.7628 (mt0) cc_final: 0.6995 (mt0) REVERT: D 189 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7984 (mtt180) REVERT: D 206 TRP cc_start: 0.7734 (t60) cc_final: 0.7486 (t60) REVERT: D 217 GLU cc_start: 0.8249 (tp30) cc_final: 0.7899 (tp30) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.4496 time to fit residues: 234.5577 Evaluate side-chains 340 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.215336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177841 restraints weight = 63517.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.183419 restraints weight = 35351.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.186951 restraints weight = 23557.997| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10880 Z= 0.234 Angle : 0.615 5.526 14852 Z= 0.326 Chirality : 0.040 0.130 1784 Planarity : 0.005 0.043 1872 Dihedral : 4.978 20.304 1536 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -2.46 (0.22), residues: 1412 helix: -1.05 (0.18), residues: 744 sheet: -3.25 (0.51), residues: 64 loop : -2.10 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 104 HIS 0.004 0.002 HIS D 323 PHE 0.024 0.002 PHE C 214 TYR 0.022 0.002 TYR C 178 ARG 0.005 0.000 ARG B 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4893.11 seconds wall clock time: 86 minutes 48.09 seconds (5208.09 seconds total)