Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 12:04:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/04_2023/5y4o_6805.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7966 2.51 5 N 2072 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G ARG 202": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 301": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12341 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "B" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "C" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "D" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "E" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "F" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "G" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1763 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 7, 'TRANS': 215} Time building chain proxies: 7.54, per 1000 atoms: 0.61 Number of scatterers: 12341 At special positions: 0 Unit cell: (100.32, 99, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2240 8.00 N 2072 7.00 C 7966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 52.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid 114 through 138 removed outlier: 3.818A pdb=" N ILE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.532A pdb=" N LEU B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.854A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'C' and resid 114 through 138 removed outlier: 3.817A pdb=" N ILE C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE C 167 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU C 220 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 3.596A pdb=" N LEU C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'D' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU D 220 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'E' and resid 114 through 138 removed outlier: 3.818A pdb=" N ILE E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 143 No H-bonds generated for 'chain 'E' and resid 141 through 143' Processing helix chain 'E' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.530A pdb=" N LEU E 220 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'F' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N PHE F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU F 220 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid 114 through 138 removed outlier: 3.819A pdb=" N ILE G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 143 No H-bonds generated for 'chain 'G' and resid 141 through 143' Processing helix chain 'G' and resid 144 through 176 removed outlier: 3.652A pdb=" N ILE G 151 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 152 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY G 153 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP G 176 " --> pdb=" O MET G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 223 removed outlier: 3.531A pdb=" N LEU G 220 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 4.853A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 265 removed outlier: 3.597A pdb=" N LEU G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU A 198 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR A 277 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU B 198 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR B 277 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU C 198 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR C 277 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU D 198 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 238 removed outlier: 3.628A pdb=" N TYR D 277 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU E 198 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR E 277 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 330 through 331 removed outlier: 6.052A pdb=" N THR E 330 " --> pdb=" O GLN F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU F 198 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR F 277 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 196 through 199 removed outlier: 3.702A pdb=" N GLU G 198 " --> pdb=" O LYS G 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 238 removed outlier: 3.627A pdb=" N TYR G 277 " --> pdb=" O MET G 289 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1533 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: 3.15 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 3 1.01 - 1.22: 350 1.22 - 1.43: 4964 1.43 - 1.64: 7164 1.64 - 1.84: 126 Bond restraints: 12607 Sorted by residual: bond pdb=" C MET E 140 " pdb=" N SER E 141 " ideal model delta sigma weight residual 1.332 0.802 0.530 1.40e-02 5.10e+03 1.44e+03 bond pdb=" C PHE E 148 " pdb=" N GLY E 149 " ideal model delta sigma weight residual 1.334 1.822 -0.487 1.42e-02 4.96e+03 1.18e+03 bond pdb=" C PHE F 148 " pdb=" N GLY F 149 " ideal model delta sigma weight residual 1.334 1.821 -0.487 1.42e-02 4.96e+03 1.17e+03 bond pdb=" C PHE B 148 " pdb=" N GLY B 149 " ideal model delta sigma weight residual 1.334 1.821 -0.486 1.42e-02 4.96e+03 1.17e+03 bond pdb=" C PHE A 148 " pdb=" N GLY A 149 " ideal model delta sigma weight residual 1.334 1.821 -0.486 1.42e-02 4.96e+03 1.17e+03 ... (remaining 12602 not shown) Histogram of bond angle deviations from ideal: 64.40 - 80.80: 6 80.80 - 97.20: 17 97.20 - 113.60: 6923 113.60 - 129.99: 10050 129.99 - 146.39: 105 Bond angle restraints: 17101 Sorted by residual: angle pdb=" CA MET A 140 " pdb=" C MET A 140 " pdb=" N SER A 141 " ideal model delta sigma weight residual 114.60 65.47 49.13 1.30e+00 5.92e-01 1.43e+03 angle pdb=" CA MET G 140 " pdb=" C MET G 140 " pdb=" N SER G 141 " ideal model delta sigma weight residual 114.60 77.96 36.64 1.30e+00 5.92e-01 7.94e+02 angle pdb=" CA MET E 140 " pdb=" C MET E 140 " pdb=" N SER E 141 " ideal model delta sigma weight residual 114.87 72.68 42.19 1.55e+00 4.16e-01 7.41e+02 angle pdb=" CA MET B 140 " pdb=" C MET B 140 " pdb=" N SER B 141 " ideal model delta sigma weight residual 114.87 73.17 41.70 1.55e+00 4.16e-01 7.24e+02 angle pdb=" CA MET F 140 " pdb=" C MET F 140 " pdb=" N SER F 141 " ideal model delta sigma weight residual 117.65 64.40 53.25 1.98e+00 2.55e-01 7.23e+02 ... (remaining 17096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 6461 21.56 - 43.13: 675 43.13 - 64.69: 270 64.69 - 86.25: 7 86.25 - 107.81: 7 Dihedral angle restraints: 7420 sinusoidal: 2926 harmonic: 4494 Sorted by residual: dihedral pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N SER C 141 " pdb=" CA SER C 141 " ideal model delta harmonic sigma weight residual 180.00 72.19 107.81 0 5.00e+00 4.00e-02 4.65e+02 dihedral pdb=" CA MET F 140 " pdb=" C MET F 140 " pdb=" N SER F 141 " pdb=" CA SER F 141 " ideal model delta harmonic sigma weight residual 180.00 77.81 102.19 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA MET D 140 " pdb=" C MET D 140 " pdb=" N SER D 141 " pdb=" CA SER D 141 " ideal model delta harmonic sigma weight residual 180.00 78.33 101.67 0 5.00e+00 4.00e-02 4.13e+02 ... (remaining 7417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1629 0.142 - 0.284: 271 0.284 - 0.425: 54 0.425 - 0.567: 6 0.567 - 0.709: 7 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CG LEU E 146 " pdb=" CB LEU E 146 " pdb=" CD1 LEU E 146 " pdb=" CD2 LEU E 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CG LEU F 146 " pdb=" CB LEU F 146 " pdb=" CD1 LEU F 146 " pdb=" CD2 LEU F 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CG LEU A 146 " pdb=" CB LEU A 146 " pdb=" CD1 LEU A 146 " pdb=" CD2 LEU A 146 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1964 not shown) Planarity restraints: 2149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 140 " 0.070 2.00e-02 2.50e+03 2.69e-01 7.21e+02 pdb=" C MET F 140 " -0.456 2.00e-02 2.50e+03 pdb=" O MET F 140 " 0.173 2.00e-02 2.50e+03 pdb=" N SER F 141 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 140 " 0.106 2.00e-02 2.50e+03 2.55e-01 6.48e+02 pdb=" C MET D 140 " -0.436 2.00e-02 2.50e+03 pdb=" O MET D 140 " 0.208 2.00e-02 2.50e+03 pdb=" N SER D 141 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 140 " -0.077 2.00e-02 2.50e+03 2.39e-01 5.69e+02 pdb=" C MET B 140 " 0.408 2.00e-02 2.50e+03 pdb=" O MET B 140 " -0.178 2.00e-02 2.50e+03 pdb=" N SER B 141 " -0.154 2.00e-02 2.50e+03 ... (remaining 2146 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.36: 46 1.36 - 2.24: 300 2.24 - 3.13: 11135 3.13 - 4.01: 30075 4.01 - 4.90: 53409 Warning: very small nonbonded interaction distances. Nonbonded interactions: 94965 Sorted by model distance: nonbonded pdb=" NE ARG C 235 " pdb=" CZ3 TRP C 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG B 235 " pdb=" CZ3 TRP B 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG G 235 " pdb=" CZ3 TRP G 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG A 235 " pdb=" CZ3 TRP A 302 " model vdw 0.471 3.420 nonbonded pdb=" NE ARG E 235 " pdb=" CZ3 TRP E 302 " model vdw 0.471 3.420 ... (remaining 94960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.050 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 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 : 0.022 0.530 12607 Z= 1.379 Angle : 2.442 53.248 17101 Z= 1.699 Chirality : 0.121 0.709 1967 Planarity : 0.022 0.269 2149 Dihedral : 19.883 107.815 4536 Min Nonbonded Distance : 0.471 Molprobity Statistics. All-atom Clashscore : 78.50 Ramachandran Plot: Outliers : 4.46 % Allowed : 7.76 % Favored : 87.78 % Rotamer Outliers : 20.31 % Cbeta Deviations : 1.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -2.08 (0.21), residues: 1547 helix: -1.35 (0.18), residues: 637 sheet: -3.24 (0.29), residues: 245 loop : -0.33 (0.26), residues: 665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 468 time to evaluate : 1.417 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 outliers start: 273 outliers final: 136 residues processed: 599 average time/residue: 0.2536 time to fit residues: 212.1773 Evaluate side-chains 501 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 365 time to evaluate : 1.477 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 23 residues processed: 136 average time/residue: 0.1754 time to fit residues: 39.3961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 234 ASN B 265 HIS C 211 ASN C 218 ASN C 264 ASN C 265 HIS C 307 GLN D 218 ASN D 264 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12607 Z= 0.238 Angle : 0.809 8.725 17101 Z= 0.440 Chirality : 0.047 0.188 1967 Planarity : 0.006 0.044 2149 Dihedral : 6.976 36.228 1701 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.69 % Favored : 93.41 % Rotamer Outliers : 5.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1547 helix: 0.20 (0.19), residues: 658 sheet: -2.66 (0.35), residues: 210 loop : -1.41 (0.22), residues: 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 461 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 23 residues processed: 491 average time/residue: 0.2445 time to fit residues: 168.9783 Evaluate side-chains 399 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 376 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1097 time to fit residues: 6.8354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN B 211 ASN B 280 GLN C 320 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 320 HIS G 320 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12607 Z= 0.188 Angle : 0.658 8.172 17101 Z= 0.355 Chirality : 0.042 0.216 1967 Planarity : 0.005 0.045 2149 Dihedral : 5.897 28.205 1701 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.66 % Favored : 92.44 % Rotamer Outliers : 6.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1547 helix: 1.14 (0.19), residues: 637 sheet: -2.39 (0.36), residues: 231 loop : -1.61 (0.21), residues: 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 401 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 50 residues processed: 451 average time/residue: 0.2228 time to fit residues: 146.8685 Evaluate side-chains 419 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 369 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.1162 time to fit residues: 12.6958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN E 211 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 329 GLN F 211 ASN ** F 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 12607 Z= 0.335 Angle : 0.750 11.100 17101 Z= 0.409 Chirality : 0.045 0.219 1967 Planarity : 0.005 0.043 2149 Dihedral : 6.227 25.652 1701 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.66 % Favored : 90.43 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1547 helix: 1.12 (0.19), residues: 630 sheet: -2.25 (0.37), residues: 224 loop : -1.40 (0.22), residues: 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 412 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 49 residues processed: 466 average time/residue: 0.2510 time to fit residues: 164.5227 Evaluate side-chains 396 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 347 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1212 time to fit residues: 12.6136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12607 Z= 0.166 Angle : 0.626 8.789 17101 Z= 0.339 Chirality : 0.042 0.230 1967 Planarity : 0.004 0.029 2149 Dihedral : 5.667 23.370 1701 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.66 % Favored : 92.44 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1547 helix: 1.44 (0.20), residues: 651 sheet: -2.25 (0.36), residues: 224 loop : -1.71 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 418 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 31 residues processed: 441 average time/residue: 0.2695 time to fit residues: 165.2786 Evaluate side-chains 389 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 358 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1338 time to fit residues: 9.1171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 306 GLN B 320 HIS ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS F 272 GLN F 280 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12607 Z= 0.165 Angle : 0.612 8.613 17101 Z= 0.328 Chirality : 0.042 0.256 1967 Planarity : 0.004 0.036 2149 Dihedral : 5.416 21.310 1701 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.27 % Favored : 92.82 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1547 helix: 1.67 (0.20), residues: 651 sheet: -2.17 (0.36), residues: 224 loop : -1.80 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 392 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 406 average time/residue: 0.3049 time to fit residues: 171.1301 Evaluate side-chains 383 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 355 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1556 time to fit residues: 9.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 0.0470 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 320 HIS ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 320 HIS C 137 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 211 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 320 HIS F 280 GLN ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.8329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 12607 Z= 0.313 Angle : 0.704 10.172 17101 Z= 0.378 Chirality : 0.045 0.235 1967 Planarity : 0.005 0.052 2149 Dihedral : 5.964 27.114 1701 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.89 % Favored : 91.21 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1547 helix: 1.66 (0.20), residues: 637 sheet: -2.07 (0.35), residues: 224 loop : -1.65 (0.24), residues: 686 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 360 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 40 residues processed: 394 average time/residue: 0.2766 time to fit residues: 150.2645 Evaluate side-chains 377 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 337 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1339 time to fit residues: 11.2277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 0.0870 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN D 329 GLN F 280 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.8606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12607 Z= 0.184 Angle : 0.637 8.616 17101 Z= 0.344 Chirality : 0.043 0.259 1967 Planarity : 0.004 0.032 2149 Dihedral : 5.604 22.400 1701 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.33 % Favored : 92.95 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1547 helix: 1.90 (0.20), residues: 637 sheet: -1.95 (0.36), residues: 224 loop : -1.67 (0.24), residues: 686 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 376 time to evaluate : 1.381 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 outliers start: 24 outliers final: 16 residues processed: 388 average time/residue: 0.2832 time to fit residues: 149.3464 Evaluate side-chains 370 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 354 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1047 time to fit residues: 5.0388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 320 HIS C 264 ASN G 320 HIS G 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.8783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12607 Z= 0.170 Angle : 0.634 9.020 17101 Z= 0.338 Chirality : 0.044 0.272 1967 Planarity : 0.004 0.050 2149 Dihedral : 5.425 21.744 1701 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.66 % Favored : 92.82 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1547 helix: 2.04 (0.20), residues: 637 sheet: -1.82 (0.35), residues: 224 loop : -1.62 (0.24), residues: 686 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 377 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 382 average time/residue: 0.2816 time to fit residues: 146.6442 Evaluate side-chains 362 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 354 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1782 time to fit residues: 4.1914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 0.0060 chunk 74 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS C 265 HIS D 329 GLN G 320 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.8911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12607 Z= 0.164 Angle : 0.636 9.816 17101 Z= 0.339 Chirality : 0.044 0.289 1967 Planarity : 0.004 0.045 2149 Dihedral : 5.360 24.070 1701 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.85 % Favored : 92.63 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1547 helix: 1.96 (0.20), residues: 651 sheet: -1.71 (0.36), residues: 224 loop : -1.83 (0.23), residues: 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 366 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 372 average time/residue: 0.2995 time to fit residues: 150.4554 Evaluate side-chains 352 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 346 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1121 time to fit residues: 3.2142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 125 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 320 HIS ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS B 306 GLN C 265 HIS ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS G 320 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.150595 restraints weight = 15673.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.153709 restraints weight = 9420.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155735 restraints weight = 6647.566| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.9038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12607 Z= 0.179 Angle : 0.643 9.192 17101 Z= 0.343 Chirality : 0.044 0.281 1967 Planarity : 0.004 0.044 2149 Dihedral : 5.359 22.272 1701 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.98 % Favored : 92.50 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1547 helix: 2.00 (0.20), residues: 651 sheet: -1.66 (0.36), residues: 224 loop : -1.77 (0.23), residues: 672 =============================================================================== Job complete usr+sys time: 3123.86 seconds wall clock time: 57 minutes 4.05 seconds (3424.05 seconds total)