Starting phenix.real_space_refine on Fri Mar 15 17:36:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/03_2024/5y4o_6805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/03_2024/5y4o_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_6805/03_2024/5y4o_6805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/03_2024/5y4o_6805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/03_2024/5y4o_6805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y4o_6805/03_2024/5y4o_6805.pdb" } resolution = 3.8 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= 0.001 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.13, per 1000 atoms: 0.58 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: 5.25 Conformation dependent library (CDL) restraints added in 2.1 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: 0.96 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: 2.71 Time building geometry restraints manager: 5.59 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: 0.120 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: 1.470 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 33.920 Find NCS groups from input model: 0.840 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- 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 % Allowed : 10.42 % Favored : 69.27 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP C 184 HIS 0.048 0.012 HIS F 137 PHE 0.096 0.008 PHE C 138 TYR 0.069 0.007 TYR D 134 ARG 0.074 0.005 ARG A 116 *********************** 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 : 1.416 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: A 268 ILE cc_start: 0.7167 (mp) cc_final: 0.6710 (mt) REVERT: B 164 LEU cc_start: 0.4522 (mp) cc_final: 0.4257 (mp) REVERT: C 174 TYR cc_start: 0.5682 (t80) cc_final: 0.5437 (t80) REVERT: D 158 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.3865 (mmt) REVERT: D 179 PHE cc_start: 0.4696 (p90) cc_final: 0.4464 (p90) REVERT: D 181 ILE cc_start: 0.7017 (mp) cc_final: 0.6810 (mt) REVERT: D 268 ILE cc_start: 0.7249 (mp) cc_final: 0.6907 (mt) REVERT: D 316 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6039 (mm) REVERT: E 237 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8327 (pp) REVERT: E 268 ILE cc_start: 0.7263 (mp) cc_final: 0.7023 (mt) REVERT: E 277 TYR cc_start: 0.8561 (m-80) cc_final: 0.8200 (m-80) REVERT: G 268 ILE cc_start: 0.7186 (mp) cc_final: 0.6971 (mt) outliers start: 273 outliers final: 136 residues processed: 599 average time/residue: 0.2455 time to fit residues: 204.4101 Evaluate side-chains 506 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 367 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 302 TRP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 302 TRP Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 302 TRP Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 302 TRP Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 235 ARG Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 270 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 302 TRP Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 236 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 243 LEU Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 270 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 302 TRP Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 330 THR 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: 0.8980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 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: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 218 ASN B 265 HIS ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 264 ASN C 265 HIS C 272 GLN C 307 GLN D 218 ASN D 264 ASN D 265 HIS D 272 GLN D 280 GLN E 264 ASN E 272 GLN E 280 GLN F 272 GLN F 280 GLN F 307 GLN G 265 HIS ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12607 Z= 0.256 Angle : 0.798 10.898 17101 Z= 0.433 Chirality : 0.046 0.198 1967 Planarity : 0.007 0.082 2149 Dihedral : 14.411 74.515 2004 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.75 % Favored : 93.34 % Rotamer: Outliers : 9.75 % Allowed : 15.25 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.86 % 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: -1.45 (0.20), residues: 1547 helix: 0.20 (0.19), residues: 651 sheet: -2.52 (0.35), residues: 210 loop : -1.52 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 184 HIS 0.007 0.002 HIS F 137 PHE 0.020 0.003 PHE G 278 TYR 0.021 0.002 TYR A 310 ARG 0.007 0.001 ARG C 120 *********************** 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 584 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 453 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.2818 (mtt) cc_final: 0.2451 (mtt) REVERT: A 172 MET cc_start: 0.7111 (tpp) cc_final: 0.6390 (ttp) REVERT: A 179 PHE cc_start: 0.4603 (p90) cc_final: 0.4231 (p90) REVERT: A 180 SER cc_start: 0.5521 (m) cc_final: 0.5050 (t) REVERT: A 268 ILE cc_start: 0.7039 (mp) cc_final: 0.6773 (mt) REVERT: B 179 PHE cc_start: 0.4350 (p90) cc_final: 0.4022 (p90) REVERT: B 180 SER cc_start: 0.5277 (m) cc_final: 0.5004 (t) REVERT: B 275 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 277 TYR cc_start: 0.8411 (m-80) cc_final: 0.8065 (m-80) REVERT: B 287 ASN cc_start: 0.7362 (m110) cc_final: 0.6934 (m110) REVERT: C 158 MET cc_start: 0.4622 (mmt) cc_final: 0.4312 (mmt) REVERT: C 234 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6584 (m110) REVERT: D 180 SER cc_start: 0.5850 (m) cc_final: 0.5216 (t) REVERT: D 314 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7314 (tt) REVERT: E 180 SER cc_start: 0.5893 (m) cc_final: 0.5620 (t) REVERT: E 237 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8236 (pt) REVERT: E 277 TYR cc_start: 0.8671 (m-80) cc_final: 0.8273 (m-80) REVERT: E 314 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7439 (tt) REVERT: F 118 MET cc_start: 0.5810 (ptt) cc_final: 0.5436 (ptp) REVERT: F 140 MET cc_start: 0.3436 (mtt) cc_final: 0.3020 (mtt) REVERT: F 277 TYR cc_start: 0.8301 (m-80) cc_final: 0.7892 (m-80) REVERT: G 172 MET cc_start: 0.6758 (tpp) cc_final: 0.5799 (ttt) REVERT: G 180 SER cc_start: 0.5538 (m) cc_final: 0.5193 (t) REVERT: G 250 LYS cc_start: 0.6227 (ptmt) cc_final: 0.6009 (pttt) outliers start: 131 outliers final: 66 residues processed: 505 average time/residue: 0.2477 time to fit residues: 175.2964 Evaluate side-chains 442 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 371 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 236 ARG Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 326 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS B 320 HIS C 320 HIS D 265 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 320 HIS F 211 ASN F 265 HIS F 280 GLN F 320 HIS G 234 ASN G 320 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12607 Z= 0.180 Angle : 0.640 7.675 17101 Z= 0.344 Chirality : 0.042 0.226 1967 Planarity : 0.004 0.034 2149 Dihedral : 10.597 70.111 1807 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.90 % Allowed : 6.79 % Favored : 92.31 % Rotamer: Outliers : 9.00 % Allowed : 19.35 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1547 helix: 1.05 (0.19), residues: 623 sheet: -2.33 (0.33), residues: 266 loop : -1.60 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 184 HIS 0.002 0.000 HIS E 137 PHE 0.017 0.002 PHE E 278 TYR 0.018 0.001 TYR G 174 ARG 0.005 0.001 ARG F 259 *********************** 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 525 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 404 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7149 (tpp) cc_final: 0.6378 (ttt) REVERT: A 179 PHE cc_start: 0.4287 (p90) cc_final: 0.4077 (p90) REVERT: B 237 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8307 (pt) REVERT: B 277 TYR cc_start: 0.8374 (m-80) cc_final: 0.8038 (m-80) REVERT: C 234 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6481 (m110) REVERT: C 237 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7617 (pp) REVERT: D 172 MET cc_start: 0.6490 (tpp) cc_final: 0.6264 (tpp) REVERT: D 173 LEU cc_start: 0.6513 (mm) cc_final: 0.6264 (mp) REVERT: D 180 SER cc_start: 0.6237 (m) cc_final: 0.5770 (t) REVERT: D 277 TYR cc_start: 0.8247 (m-80) cc_final: 0.7928 (m-80) REVERT: E 186 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6717 (ptt90) REVERT: E 237 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8253 (pt) REVERT: E 277 TYR cc_start: 0.8524 (m-80) cc_final: 0.8066 (m-80) REVERT: F 118 MET cc_start: 0.5469 (ptt) cc_final: 0.5099 (ptp) REVERT: F 158 MET cc_start: 0.4111 (mmt) cc_final: 0.3881 (mmt) REVERT: F 172 MET cc_start: 0.6794 (tpp) cc_final: 0.6154 (ttt) REVERT: F 277 TYR cc_start: 0.8225 (m-80) cc_final: 0.7906 (m-80) REVERT: G 172 MET cc_start: 0.6831 (tpp) cc_final: 0.5703 (ttp) REVERT: G 237 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8679 (pt) outliers start: 121 outliers final: 75 residues processed: 460 average time/residue: 0.2319 time to fit residues: 151.9721 Evaluate side-chains 427 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 346 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 236 ARG Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 299 TRP Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS E 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12607 Z= 0.208 Angle : 0.638 9.809 17101 Z= 0.348 Chirality : 0.043 0.242 1967 Planarity : 0.004 0.030 2149 Dihedral : 8.850 60.948 1767 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.24 % Favored : 91.86 % Rotamer: Outliers : 8.56 % Allowed : 20.98 % Favored : 70.46 % 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: -0.70 (0.21), residues: 1547 helix: 1.39 (0.19), residues: 651 sheet: -2.24 (0.35), residues: 231 loop : -1.69 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 184 HIS 0.004 0.001 HIS G 137 PHE 0.011 0.001 PHE D 278 TYR 0.017 0.001 TYR B 174 ARG 0.016 0.001 ARG G 271 *********************** 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 524 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 409 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7125 (tpp) cc_final: 0.6258 (ttt) REVERT: A 215 TYR cc_start: 0.8012 (m-80) cc_final: 0.7734 (m-80) REVERT: B 237 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8362 (pt) REVERT: B 275 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (mp) REVERT: B 277 TYR cc_start: 0.8525 (m-80) cc_final: 0.8051 (m-80) REVERT: B 287 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7545 (m-40) REVERT: C 234 ASN cc_start: 0.7473 (m110) cc_final: 0.6977 (m110) REVERT: D 281 PHE cc_start: 0.8413 (t80) cc_final: 0.8185 (t80) REVERT: E 161 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5310 (tppt) REVERT: E 237 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8489 (pt) REVERT: F 172 MET cc_start: 0.7054 (tpp) cc_final: 0.6157 (ttt) REVERT: F 277 TYR cc_start: 0.8367 (m-80) cc_final: 0.7859 (m-80) REVERT: G 172 MET cc_start: 0.6906 (tpp) cc_final: 0.5683 (ttt) REVERT: G 236 ARG cc_start: 0.7517 (ttp-170) cc_final: 0.7304 (ttp-170) REVERT: G 237 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8551 (pt) REVERT: G 286 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7271 (tp) REVERT: G 287 ASN cc_start: 0.8650 (p0) cc_final: 0.7873 (p0) outliers start: 115 outliers final: 79 residues processed: 472 average time/residue: 0.2449 time to fit residues: 162.3809 Evaluate side-chains 447 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 361 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER 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: 3.9990 chunk 2 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN G 211 ASN G 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.7223 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= 0.215 Angle : 0.616 8.219 17101 Z= 0.336 Chirality : 0.043 0.242 1967 Planarity : 0.004 0.069 2149 Dihedral : 8.087 59.778 1747 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.27 % Favored : 90.82 % Rotamer: Outliers : 9.75 % Allowed : 21.58 % Favored : 68.68 % 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: -0.60 (0.21), residues: 1547 helix: 1.68 (0.20), residues: 651 sheet: -2.08 (0.36), residues: 224 loop : -1.95 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 184 HIS 0.002 0.001 HIS E 137 PHE 0.010 0.001 PHE F 278 TYR 0.022 0.001 TYR G 174 ARG 0.007 0.001 ARG E 271 *********************** 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 505 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 374 time to evaluate : 1.364 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: A 172 MET cc_start: 0.7324 (tpp) cc_final: 0.6360 (ttt) REVERT: A 232 MET cc_start: 0.7337 (mmm) cc_final: 0.6698 (mmm) REVERT: B 224 ILE cc_start: 0.8390 (pt) cc_final: 0.8151 (pt) REVERT: B 237 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8623 (pt) REVERT: C 234 ASN cc_start: 0.7535 (m110) cc_final: 0.7175 (m110) REVERT: D 161 LYS cc_start: 0.5654 (OUTLIER) cc_final: 0.5280 (tppt) REVERT: D 172 MET cc_start: 0.6862 (tpp) cc_final: 0.6561 (tpp) REVERT: E 237 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8478 (pt) REVERT: E 277 TYR cc_start: 0.8555 (m-80) cc_final: 0.8064 (m-80) REVERT: F 172 MET cc_start: 0.7090 (tpp) cc_final: 0.6261 (ttt) REVERT: F 174 TYR cc_start: 0.5174 (t80) cc_final: 0.4782 (t80) REVERT: F 277 TYR cc_start: 0.8399 (m-80) cc_final: 0.7848 (m-80) REVERT: G 172 MET cc_start: 0.7044 (tpp) cc_final: 0.5613 (ttt) REVERT: G 173 LEU cc_start: 0.6129 (mp) cc_final: 0.5923 (mm) REVERT: G 237 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8565 (pt) REVERT: G 250 LYS cc_start: 0.5729 (ptmt) cc_final: 0.5452 (ptmt) REVERT: G 280 GLN cc_start: 0.6859 (tp40) cc_final: 0.6293 (tp40) outliers start: 131 outliers final: 98 residues processed: 460 average time/residue: 0.2532 time to fit residues: 163.3623 Evaluate side-chains 448 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 346 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0020 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.9930 ------------------------------------------------------------------------------- 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 ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 265 HIS F 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12607 Z= 0.161 Angle : 0.592 8.058 17101 Z= 0.319 Chirality : 0.042 0.250 1967 Planarity : 0.004 0.057 2149 Dihedral : 7.557 58.133 1743 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.05 % Favored : 92.05 % Rotamer: Outliers : 8.63 % Allowed : 24.26 % Favored : 67.11 % 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: -0.53 (0.21), residues: 1547 helix: 1.85 (0.20), residues: 651 sheet: -2.14 (0.35), residues: 224 loop : -2.00 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 184 HIS 0.002 0.000 HIS E 265 PHE 0.016 0.001 PHE E 278 TYR 0.022 0.001 TYR C 174 ARG 0.012 0.001 ARG C 244 *********************** 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 493 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 377 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7270 (tpp) cc_final: 0.6400 (ttp) REVERT: A 289 MET cc_start: 0.8301 (tmm) cc_final: 0.8029 (tmm) REVERT: B 201 TRP cc_start: 0.6997 (m100) cc_final: 0.6720 (m100) REVERT: B 224 ILE cc_start: 0.8427 (pt) cc_final: 0.8189 (pt) REVERT: B 237 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8502 (pt) REVERT: B 287 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7466 (m-40) REVERT: C 234 ASN cc_start: 0.7478 (m110) cc_final: 0.7221 (m110) REVERT: C 333 MET cc_start: 0.5482 (mmm) cc_final: 0.5261 (mmp) REVERT: D 172 MET cc_start: 0.6926 (tpp) cc_final: 0.6681 (tpp) REVERT: E 237 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8451 (pt) REVERT: F 172 MET cc_start: 0.7013 (tpp) cc_final: 0.6205 (ttt) REVERT: F 174 TYR cc_start: 0.5147 (t80) cc_final: 0.4860 (t80) REVERT: F 277 TYR cc_start: 0.8390 (m-80) cc_final: 0.7845 (m-80) REVERT: F 333 MET cc_start: 0.5408 (mmm) cc_final: 0.4887 (mmp) REVERT: G 172 MET cc_start: 0.6956 (tpp) cc_final: 0.5508 (ttt) REVERT: G 237 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8600 (pt) REVERT: G 280 GLN cc_start: 0.6939 (tp40) cc_final: 0.6430 (tp40) outliers start: 116 outliers final: 88 residues processed: 451 average time/residue: 0.2638 time to fit residues: 165.6496 Evaluate side-chains 449 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 357 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 TRP Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 326 PHE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 206 ILE Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 326 PHE Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 137 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN F 280 GLN G 228 ASN G 320 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12607 Z= 0.185 Angle : 0.607 9.426 17101 Z= 0.326 Chirality : 0.043 0.256 1967 Planarity : 0.004 0.040 2149 Dihedral : 7.315 56.289 1739 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.60 % Rotamer: Outliers : 8.18 % Allowed : 25.22 % Favored : 66.59 % 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: -0.50 (0.22), residues: 1547 helix: 1.93 (0.20), residues: 651 sheet: -2.17 (0.34), residues: 224 loop : -2.03 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 184 HIS 0.002 0.001 HIS E 265 PHE 0.011 0.001 PHE E 278 TYR 0.024 0.001 TYR B 174 ARG 0.006 0.001 ARG C 244 *********************** 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 476 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 366 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.3744 (m-10) cc_final: 0.3500 (m-80) REVERT: A 172 MET cc_start: 0.7250 (tpp) cc_final: 0.6318 (ttt) REVERT: B 201 TRP cc_start: 0.7039 (m100) cc_final: 0.6737 (m100) REVERT: B 224 ILE cc_start: 0.8601 (pt) cc_final: 0.8380 (pt) REVERT: B 237 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8460 (pt) REVERT: B 275 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 287 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7582 (m-40) REVERT: C 234 ASN cc_start: 0.7552 (m110) cc_final: 0.7135 (m110) REVERT: D 161 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5433 (tppt) REVERT: D 172 MET cc_start: 0.6922 (tpp) cc_final: 0.6704 (tpp) REVERT: E 174 TYR cc_start: 0.5653 (t80) cc_final: 0.5354 (t80) REVERT: F 172 MET cc_start: 0.7019 (tpp) cc_final: 0.6137 (ttt) REVERT: F 173 LEU cc_start: 0.6694 (tp) cc_final: 0.6480 (mm) REVERT: F 174 TYR cc_start: 0.5310 (t80) cc_final: 0.5051 (t80) REVERT: F 232 MET cc_start: 0.7123 (mtp) cc_final: 0.6391 (mmm) REVERT: F 277 TYR cc_start: 0.8432 (m-80) cc_final: 0.7873 (m-80) REVERT: G 172 MET cc_start: 0.6944 (tpp) cc_final: 0.5485 (ttt) REVERT: G 173 LEU cc_start: 0.6108 (mm) cc_final: 0.5745 (mt) REVERT: G 212 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7823 (mtt180) REVERT: G 237 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8635 (pt) REVERT: G 280 GLN cc_start: 0.7065 (tp40) cc_final: 0.6513 (tp40) outliers start: 110 outliers final: 90 residues processed: 440 average time/residue: 0.2599 time to fit residues: 161.6970 Evaluate side-chains 456 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 361 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN F 280 GLN G 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12607 Z= 0.186 Angle : 0.606 7.969 17101 Z= 0.325 Chirality : 0.043 0.262 1967 Planarity : 0.004 0.040 2149 Dihedral : 6.872 56.775 1727 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.89 % Favored : 91.53 % Rotamer: Outliers : 7.66 % Allowed : 26.26 % Favored : 66.07 % 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: -0.44 (0.22), residues: 1547 helix: 1.98 (0.20), residues: 651 sheet: -2.13 (0.34), residues: 224 loop : -2.01 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 184 HIS 0.002 0.001 HIS E 265 PHE 0.011 0.001 PHE E 278 TYR 0.027 0.002 TYR D 174 ARG 0.006 0.000 ARG C 244 *********************** 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 482 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 379 time to evaluate : 1.386 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: A 172 MET cc_start: 0.7236 (tpp) cc_final: 0.6354 (ttt) REVERT: B 201 TRP cc_start: 0.7085 (m100) cc_final: 0.6796 (m100) REVERT: B 224 ILE cc_start: 0.8617 (pt) cc_final: 0.8410 (pt) REVERT: B 237 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8541 (pt) REVERT: C 234 ASN cc_start: 0.7483 (m110) cc_final: 0.7137 (m110) REVERT: D 247 ASP cc_start: 0.4607 (m-30) cc_final: 0.4116 (m-30) REVERT: F 277 TYR cc_start: 0.8494 (m-80) cc_final: 0.7940 (m-80) REVERT: F 333 MET cc_start: 0.5560 (mmm) cc_final: 0.5228 (mmm) REVERT: G 172 MET cc_start: 0.6963 (tpp) cc_final: 0.5688 (ttt) REVERT: G 237 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8605 (pt) REVERT: G 280 GLN cc_start: 0.7264 (tp40) cc_final: 0.6772 (tp40) REVERT: G 286 LEU cc_start: 0.7393 (mt) cc_final: 0.7101 (tt) outliers start: 103 outliers final: 82 residues processed: 450 average time/residue: 0.2439 time to fit residues: 153.4131 Evaluate side-chains 449 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 365 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 287 ASN Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 0.0570 chunk 90 optimal weight: 30.0000 overall best weight: 2.0104 ------------------------------------------------------------------------------- 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 ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.8433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12607 Z= 0.225 Angle : 0.638 8.194 17101 Z= 0.343 Chirality : 0.044 0.267 1967 Planarity : 0.004 0.042 2149 Dihedral : 6.912 57.960 1721 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.34 % Favored : 91.21 % Rotamer: Outliers : 7.37 % Allowed : 27.01 % Favored : 65.62 % 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: -0.45 (0.22), residues: 1547 helix: 1.94 (0.20), residues: 651 sheet: -2.12 (0.34), residues: 224 loop : -1.98 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 201 HIS 0.002 0.001 HIS G 320 PHE 0.013 0.001 PHE E 278 TYR 0.028 0.002 TYR B 174 ARG 0.007 0.000 ARG C 244 *********************** 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 478 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 379 time to evaluate : 1.393 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: A 172 MET cc_start: 0.7221 (tpp) cc_final: 0.6370 (ttt) REVERT: B 201 TRP cc_start: 0.7165 (m100) cc_final: 0.6832 (m100) REVERT: B 237 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8510 (pt) REVERT: C 234 ASN cc_start: 0.7510 (m110) cc_final: 0.7219 (m110) REVERT: D 173 LEU cc_start: 0.6098 (mm) cc_final: 0.5737 (mp) REVERT: D 203 ILE cc_start: 0.7498 (pp) cc_final: 0.7291 (pt) REVERT: D 247 ASP cc_start: 0.4731 (m-30) cc_final: 0.4212 (m-30) REVERT: F 172 MET cc_start: 0.7037 (tpp) cc_final: 0.6371 (ttt) REVERT: F 277 TYR cc_start: 0.8503 (m-80) cc_final: 0.7836 (m-80) REVERT: F 333 MET cc_start: 0.5635 (mmm) cc_final: 0.5308 (mmm) REVERT: G 232 MET cc_start: 0.7971 (mmm) cc_final: 0.7687 (mmm) REVERT: G 237 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8697 (pt) REVERT: G 280 GLN cc_start: 0.7272 (tp40) cc_final: 0.6538 (tp40) REVERT: G 287 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.7808 (p0) outliers start: 99 outliers final: 83 residues processed: 445 average time/residue: 0.2422 time to fit residues: 150.5442 Evaluate side-chains 447 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 361 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 287 ASN Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.8602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12607 Z= 0.206 Angle : 0.639 8.130 17101 Z= 0.343 Chirality : 0.044 0.276 1967 Planarity : 0.004 0.050 2149 Dihedral : 6.660 59.372 1717 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.56 % Favored : 91.79 % Rotamer: Outliers : 6.55 % Allowed : 27.98 % Favored : 65.48 % 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: -0.44 (0.22), residues: 1547 helix: 1.96 (0.20), residues: 651 sheet: -2.14 (0.33), residues: 224 loop : -1.97 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 184 HIS 0.003 0.000 HIS E 265 PHE 0.012 0.001 PHE E 278 TYR 0.028 0.002 TYR C 174 ARG 0.015 0.000 ARG C 244 ********************** 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 460 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 372 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7186 (tpp) cc_final: 0.6367 (ttt) REVERT: B 201 TRP cc_start: 0.7206 (m100) cc_final: 0.6852 (m100) REVERT: B 237 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (pt) REVERT: B 287 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7680 (m-40) REVERT: C 173 LEU cc_start: 0.6333 (mp) cc_final: 0.6093 (mm) REVERT: C 234 ASN cc_start: 0.7387 (m110) cc_final: 0.7054 (m110) REVERT: D 247 ASP cc_start: 0.4723 (m-30) cc_final: 0.4103 (m-30) REVERT: F 140 MET cc_start: 0.2368 (ttm) cc_final: 0.2125 (ttm) REVERT: F 172 MET cc_start: 0.7248 (tpp) cc_final: 0.6506 (ttt) REVERT: F 277 TYR cc_start: 0.8488 (m-80) cc_final: 0.7825 (m-80) REVERT: F 333 MET cc_start: 0.5683 (mmm) cc_final: 0.5309 (mmm) REVERT: G 232 MET cc_start: 0.8227 (mmm) cc_final: 0.7983 (mmm) REVERT: G 237 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8698 (pt) REVERT: G 280 GLN cc_start: 0.7285 (tp40) cc_final: 0.6839 (tp40) REVERT: G 329 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8145 (mt0) outliers start: 88 outliers final: 79 residues processed: 436 average time/residue: 0.2516 time to fit residues: 153.0729 Evaluate side-chains 448 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 366 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 287 ASN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain G residue 218 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 320 HIS ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.184905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.152166 restraints weight = 15616.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.155049 restraints weight = 9162.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156984 restraints weight = 6293.322| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.8808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12607 Z= 0.178 Angle : 0.639 8.275 17101 Z= 0.340 Chirality : 0.044 0.275 1967 Planarity : 0.004 0.058 2149 Dihedral : 6.568 58.310 1717 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.89 % Favored : 91.47 % Rotamer: Outliers : 5.73 % Allowed : 28.87 % Favored : 65.40 % 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: -0.35 (0.22), residues: 1547 helix: 2.03 (0.20), residues: 651 sheet: -2.09 (0.33), residues: 224 loop : -1.92 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 184 HIS 0.003 0.000 HIS E 265 PHE 0.012 0.001 PHE F 278 TYR 0.029 0.002 TYR D 174 ARG 0.015 0.001 ARG C 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.57 seconds wall clock time: 59 minutes 51.99 seconds (3591.99 seconds total)