Starting phenix.real_space_refine on Sun Feb 18 22:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acf_9590/02_2024/6acf_9590.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 136 5.16 5 C 14512 2.51 5 N 4152 2.21 5 O 4344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 365": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "G ARG 363": "NH1" <-> "NH2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "H TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 326": "NH1" <-> "NH2" Residue "H ARG 363": "NH1" <-> "NH2" Residue "H ARG 365": "NH1" <-> "NH2" Residue "H ARG 367": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23144 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "B" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "C" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "D" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "E" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "F" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "G" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Chain: "H" Number of atoms: 2893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Conformer: "B" Number of residues, atoms: 367, 2845 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} bond proxies already assigned to first conformer: 2840 Time building chain proxies: 22.98, per 1000 atoms: 0.99 Number of scatterers: 23144 At special positions: 0 Unit cell: (126.896, 126.896, 119.504, 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 136 16.00 O 4344 8.00 N 4152 7.00 C 14512 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: 8.70 Conformation dependent library (CDL) restraints added in 8.2 seconds 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5408 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 51.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.725A pdb=" N GLN A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.187A pdb=" N ALA B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN B 250 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 300 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR C 10 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 4.046A pdb=" N PHE C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN C 250 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 300 Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 312 through 328 Processing helix chain 'C' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR D 10 " --> pdb=" O TYR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL D 209 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.725A pdb=" N GLN D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 300 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 312 through 328 Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA E 149 " --> pdb=" O ASN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL E 209 " --> pdb=" O ASN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.723A pdb=" N GLN E 250 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 297 through 300 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 312 through 328 Processing helix chain 'E' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL F 209 " --> pdb=" O ASN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.723A pdb=" N GLN F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY F 270 " --> pdb=" O GLU F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE F 286 " --> pdb=" O PRO F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 297 through 300 Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 312 through 328 Processing helix chain 'F' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR G 10 " --> pdb=" O TYR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 145 through 167 removed outlier: 4.020A pdb=" N ALA G 149 " --> pdb=" O ASN G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 196 Processing helix chain 'G' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL G 209 " --> pdb=" O ASN G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 removed outlier: 3.724A pdb=" N GLN G 250 " --> pdb=" O THR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 277 removed outlier: 3.721A pdb=" N GLY G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 297 through 300 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 312 through 328 Processing helix chain 'G' and resid 330 through 350 removed outlier: 3.776A pdb=" N ASP G 336 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG G 350 " --> pdb=" O MET G 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 11 removed outlier: 3.816A pdb=" N TYR H 10 " --> pdb=" O TYR H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 72 removed outlier: 4.183A pdb=" N ALA H 54 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 removed outlier: 4.045A pdb=" N PHE H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 145 through 167 removed outlier: 4.021A pdb=" N ALA H 149 " --> pdb=" O ASN H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 205 through 217 removed outlier: 3.679A pdb=" N VAL H 209 " --> pdb=" O ASN H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.726A pdb=" N GLN H 250 " --> pdb=" O THR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 277 removed outlier: 3.722A pdb=" N GLY H 270 " --> pdb=" O GLU H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 removed outlier: 3.526A pdb=" N ILE H 286 " --> pdb=" O PRO H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 297 through 300 Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 312 through 328 Processing helix chain 'H' and resid 330 through 350 removed outlier: 3.775A pdb=" N ASP H 336 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG H 350 " --> pdb=" O MET H 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA A 39 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA A 113 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY A 41 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 40 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR A 81 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY A 42 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE A 83 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG A 44 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 78 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS A 26 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS B 26 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY B 78 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU B 40 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR B 81 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY B 42 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE B 83 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA B 39 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA B 113 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY B 41 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL A 175 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA A 235 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 177 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL B 175 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA B 235 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 177 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA C 39 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA C 113 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY C 41 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU C 40 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR C 81 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY C 42 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 83 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG C 44 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY C 78 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS C 26 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 26 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY D 78 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU D 40 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR D 81 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY D 42 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE D 83 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG D 44 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA D 39 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA D 113 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY D 41 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL C 175 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA C 235 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA C 177 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 198 through 202 removed outlier: 6.404A pdb=" N VAL D 175 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA D 235 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA D 177 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA E 39 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA E 113 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY E 41 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU E 40 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR E 81 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 42 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 83 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG E 44 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY E 78 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS E 26 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS F 26 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY F 78 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU F 40 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR F 81 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY F 42 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE F 83 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG F 44 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA F 39 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA F 113 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY F 41 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL E 175 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA E 235 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA E 177 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL F 175 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA F 235 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA F 177 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 110 through 114 removed outlier: 6.086A pdb=" N ALA G 39 " --> pdb=" O ILE G 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA G 113 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY G 41 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU G 40 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR G 81 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY G 42 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE G 83 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG G 44 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY G 78 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS G 26 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS H 26 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY H 78 " --> pdb=" O HIS H 32 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU H 40 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR H 81 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY H 42 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE H 83 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG H 44 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA H 39 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA H 113 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY H 41 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL G 175 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA G 235 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA G 177 " --> pdb=" O ALA G 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 198 through 202 removed outlier: 6.403A pdb=" N VAL H 175 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA H 235 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA H 177 " --> pdb=" O ALA H 235 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 9.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.45: 3517 1.45 - 1.57: 12585 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 23584 Sorted by residual: bond pdb=" C MET F 123 " pdb=" N ASP F 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET E 123 " pdb=" N ASP E 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET G 123 " pdb=" N ASP G 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET C 123 " pdb=" N ASP C 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 bond pdb=" C MET D 123 " pdb=" N ASP D 124 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 ... (remaining 23579 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.02: 304 104.02 - 111.50: 9254 111.50 - 118.97: 9438 118.97 - 126.44: 12652 126.44 - 133.91: 192 Bond angle restraints: 31840 Sorted by residual: angle pdb=" N ASP B 124 " pdb=" CA ASP B 124 " pdb=" C ASP B 124 " ideal model delta sigma weight residual 114.62 110.15 4.47 1.14e+00 7.69e-01 1.54e+01 angle pdb=" N ASP F 124 " pdb=" CA ASP F 124 " pdb=" C ASP F 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP D 124 " pdb=" CA ASP D 124 " pdb=" C ASP D 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP E 124 " pdb=" CA ASP E 124 " pdb=" C ASP E 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 angle pdb=" N ASP H 124 " pdb=" CA ASP H 124 " pdb=" C ASP H 124 " ideal model delta sigma weight residual 114.62 110.18 4.44 1.14e+00 7.69e-01 1.52e+01 ... (remaining 31835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.38: 12988 11.38 - 22.76: 1019 22.76 - 34.14: 265 34.14 - 45.53: 80 45.53 - 56.91: 56 Dihedral angle restraints: 14408 sinusoidal: 5832 harmonic: 8576 Sorted by residual: dihedral pdb=" CA VAL F 120 " pdb=" C VAL F 120 " pdb=" N ALA F 121 " pdb=" CA ALA F 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL D 120 " pdb=" C VAL D 120 " pdb=" N ALA D 121 " pdb=" CA ALA D 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL E 120 " pdb=" C VAL E 120 " pdb=" N ALA E 121 " pdb=" CA ALA E 121 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 14405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1757 0.037 - 0.074: 996 0.074 - 0.111: 492 0.111 - 0.148: 138 0.148 - 0.185: 33 Chirality restraints: 3416 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU D 25 " pdb=" CB LEU D 25 " pdb=" CD1 LEU D 25 " pdb=" CD2 LEU D 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 3413 not shown) Planarity restraints: 4240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE B 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE G 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE G 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE G 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 102 " -0.014 2.00e-02 2.50e+03 1.76e-02 5.41e+00 pdb=" CG PHE A 102 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 102 " -0.001 2.00e-02 2.50e+03 ... (remaining 4237 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6114 2.80 - 3.33: 19843 3.33 - 3.85: 38006 3.85 - 4.38: 45219 4.38 - 4.90: 79681 Nonbonded interactions: 188863 Sorted by model distance: nonbonded pdb=" OH TYR A 48 " pdb=" OD2 ASP A 57 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR B 48 " pdb=" OD2 ASP B 57 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR D 48 " pdb=" OD2 ASP D 57 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR G 48 " pdb=" OD2 ASP G 57 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR E 48 " pdb=" OD2 ASP E 57 " model vdw 2.281 2.440 ... (remaining 188858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'B' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'C' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'D' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'E' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'F' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'G' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) selection = (chain 'H' and (resid 1 through 43 or resid 45 through 62 or resid 64 through 26 \ 7 or resid 269 through 325 or resid 327 through 346 or resid 348 through 364 or \ resid 366 through 367)) } 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.460 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: 2.970 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 74.910 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.130 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.008 0.065 23584 Z= 0.512 Angle : 0.955 9.222 31840 Z= 0.521 Chirality : 0.057 0.185 3416 Planarity : 0.007 0.056 4240 Dihedral : 10.115 56.906 9000 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.68 % Allowed : 3.34 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.12), residues: 2968 helix: -2.16 (0.10), residues: 1408 sheet: -1.33 (0.23), residues: 464 loop : -2.38 (0.15), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 46 HIS 0.010 0.002 HIS B 269 PHE 0.040 0.005 PHE B 102 TYR 0.021 0.004 TYR G 299 ARG 0.015 0.002 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 2.483 Fit side-chains REVERT: A 46 TRP cc_start: 0.7813 (t-100) cc_final: 0.7450 (t-100) REVERT: A 263 GLN cc_start: 0.8858 (mt0) cc_final: 0.8628 (mt0) REVERT: A 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7389 (mmt180) REVERT: B 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7453 (t-100) REVERT: B 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8629 (mt0) REVERT: B 303 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7386 (mmt180) REVERT: C 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7449 (t-100) REVERT: C 263 GLN cc_start: 0.8861 (mt0) cc_final: 0.8630 (mt0) REVERT: C 303 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7386 (mmt180) REVERT: D 46 TRP cc_start: 0.7814 (t-100) cc_final: 0.7452 (t-100) REVERT: D 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8628 (mt0) REVERT: D 303 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7387 (mmt180) REVERT: E 46 TRP cc_start: 0.7814 (t-100) cc_final: 0.7448 (t-100) REVERT: E 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8626 (mt0) REVERT: E 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7384 (mmt180) REVERT: F 46 TRP cc_start: 0.7813 (t-100) cc_final: 0.7450 (t-100) REVERT: F 263 GLN cc_start: 0.8859 (mt0) cc_final: 0.8626 (mt0) REVERT: F 303 ARG cc_start: 0.7895 (tpt170) cc_final: 0.7389 (mmt180) REVERT: G 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7449 (t-100) REVERT: G 263 GLN cc_start: 0.8860 (mt0) cc_final: 0.8627 (mt0) REVERT: G 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7389 (mmt180) REVERT: H 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7452 (t-100) REVERT: H 263 GLN cc_start: 0.8857 (mt0) cc_final: 0.8652 (mt0) REVERT: H 303 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7392 (mmt180) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 1.3457 time to fit residues: 919.2896 Evaluate side-chains 376 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 261 ASN A 293 ASN A 316 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 224 ASN B 261 ASN B 293 ASN B 316 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 261 ASN C 293 ASN C 316 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN D 261 ASN D 293 ASN D 316 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN E 261 ASN E 293 ASN E 316 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 261 ASN F 293 ASN F 316 ASN ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 261 ASN G 293 ASN G 316 ASN ** G 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN H 224 ASN H 261 ASN H 293 ASN H 316 ASN ** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23584 Z= 0.174 Angle : 0.553 5.907 31840 Z= 0.301 Chirality : 0.043 0.135 3416 Planarity : 0.004 0.039 4240 Dihedral : 5.116 28.532 3392 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.07 % Allowed : 11.44 % Favored : 86.49 % 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: -1.39 (0.14), residues: 2968 helix: -0.19 (0.12), residues: 1504 sheet: -0.94 (0.23), residues: 472 loop : -1.89 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP G 46 HIS 0.004 0.001 HIS F 269 PHE 0.014 0.002 PHE C 102 TYR 0.016 0.002 TYR G 314 ARG 0.003 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 415 time to evaluate : 2.535 Fit side-chains REVERT: A 46 TRP cc_start: 0.7799 (t-100) cc_final: 0.7436 (t-100) REVERT: A 115 ASP cc_start: 0.8255 (t70) cc_final: 0.7634 (t0) REVERT: A 303 ARG cc_start: 0.7931 (tpt170) cc_final: 0.7386 (mmt180) REVERT: A 355 GLN cc_start: 0.9112 (pt0) cc_final: 0.8820 (pt0) REVERT: B 46 TRP cc_start: 0.7800 (t-100) cc_final: 0.7434 (t-100) REVERT: B 115 ASP cc_start: 0.8257 (t70) cc_final: 0.7640 (t0) REVERT: B 303 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7382 (mmt180) REVERT: B 355 GLN cc_start: 0.9108 (pt0) cc_final: 0.8824 (pt0) REVERT: C 46 TRP cc_start: 0.7800 (t-100) cc_final: 0.7435 (t-100) REVERT: C 115 ASP cc_start: 0.8252 (t70) cc_final: 0.7634 (t0) REVERT: C 303 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7384 (mmt180) REVERT: C 355 GLN cc_start: 0.9110 (pt0) cc_final: 0.8814 (pt0) REVERT: D 46 TRP cc_start: 0.7799 (t-100) cc_final: 0.7435 (t-100) REVERT: D 115 ASP cc_start: 0.8255 (t70) cc_final: 0.7640 (t0) REVERT: D 303 ARG cc_start: 0.7932 (tpt170) cc_final: 0.7379 (mmt180) REVERT: D 355 GLN cc_start: 0.9109 (pt0) cc_final: 0.8826 (pt0) REVERT: E 46 TRP cc_start: 0.7796 (t-100) cc_final: 0.7431 (t-100) REVERT: E 115 ASP cc_start: 0.8252 (t70) cc_final: 0.7634 (t0) REVERT: E 303 ARG cc_start: 0.7928 (tpt170) cc_final: 0.7377 (mmt180) REVERT: E 355 GLN cc_start: 0.9107 (pt0) cc_final: 0.8816 (pt0) REVERT: F 46 TRP cc_start: 0.7800 (t-100) cc_final: 0.7435 (t-100) REVERT: F 115 ASP cc_start: 0.8256 (t70) cc_final: 0.7640 (t0) REVERT: F 303 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7382 (mmt180) REVERT: F 355 GLN cc_start: 0.9108 (pt0) cc_final: 0.8823 (pt0) REVERT: G 46 TRP cc_start: 0.7798 (t-100) cc_final: 0.7435 (t-100) REVERT: G 115 ASP cc_start: 0.8255 (t70) cc_final: 0.7635 (t0) REVERT: G 303 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7380 (mmt180) REVERT: G 355 GLN cc_start: 0.9110 (pt0) cc_final: 0.8819 (pt0) REVERT: H 46 TRP cc_start: 0.7799 (t-100) cc_final: 0.7436 (t-100) REVERT: H 115 ASP cc_start: 0.8255 (t70) cc_final: 0.7638 (t0) REVERT: H 303 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7384 (mmt180) REVERT: H 355 GLN cc_start: 0.9105 (pt0) cc_final: 0.8821 (pt0) outliers start: 33 outliers final: 1 residues processed: 432 average time/residue: 1.3945 time to fit residues: 684.9956 Evaluate side-chains 377 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 107 ASN A 179 GLN A 224 ASN A 359 HIS B 104 GLN B 107 ASN B 179 GLN B 224 ASN B 359 HIS C 104 GLN C 107 ASN C 179 GLN C 224 ASN C 359 HIS D 104 GLN D 107 ASN D 179 GLN D 224 ASN D 359 HIS E 104 GLN E 107 ASN E 179 GLN E 224 ASN E 359 HIS F 104 GLN F 107 ASN F 179 GLN F 224 ASN F 359 HIS G 104 GLN G 107 ASN G 179 GLN G 224 ASN G 359 HIS H 104 GLN H 107 ASN H 179 GLN H 224 ASN H 359 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 23584 Z= 0.614 Angle : 0.743 8.590 31840 Z= 0.393 Chirality : 0.052 0.172 3416 Planarity : 0.007 0.063 4240 Dihedral : 5.371 25.736 3392 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.17 % Allowed : 12.04 % Favored : 84.80 % 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: -0.93 (0.15), residues: 2968 helix: 0.44 (0.13), residues: 1448 sheet: -1.00 (0.24), residues: 456 loop : -1.85 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 46 HIS 0.004 0.001 HIS C 358 PHE 0.020 0.003 PHE D 4 TYR 0.024 0.003 TYR F 284 ARG 0.011 0.002 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 408 time to evaluate : 2.740 Fit side-chains REVERT: A 46 TRP cc_start: 0.7870 (t-100) cc_final: 0.7553 (t-100) REVERT: A 115 ASP cc_start: 0.8297 (t70) cc_final: 0.7681 (t0) REVERT: A 303 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7485 (mmt180) REVERT: A 360 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8959 (tt) REVERT: B 46 TRP cc_start: 0.7873 (t-100) cc_final: 0.7552 (t-100) REVERT: B 115 ASP cc_start: 0.8300 (t70) cc_final: 0.7684 (t0) REVERT: B 303 ARG cc_start: 0.8018 (tpt170) cc_final: 0.7491 (mmt180) REVERT: B 360 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8958 (tt) REVERT: C 46 TRP cc_start: 0.7872 (t-100) cc_final: 0.7552 (t-100) REVERT: C 115 ASP cc_start: 0.8296 (t70) cc_final: 0.7679 (t0) REVERT: C 303 ARG cc_start: 0.8006 (tpt170) cc_final: 0.7483 (mmt180) REVERT: C 360 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8962 (tt) REVERT: D 46 TRP cc_start: 0.7870 (t-100) cc_final: 0.7552 (t-100) REVERT: D 115 ASP cc_start: 0.8302 (t70) cc_final: 0.7685 (t0) REVERT: D 303 ARG cc_start: 0.8014 (tpt170) cc_final: 0.7490 (mmt180) REVERT: D 360 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8960 (tt) REVERT: E 46 TRP cc_start: 0.7869 (t-100) cc_final: 0.7547 (t-100) REVERT: E 115 ASP cc_start: 0.8298 (t70) cc_final: 0.7679 (t0) REVERT: E 303 ARG cc_start: 0.8008 (tpt170) cc_final: 0.7486 (mmt180) REVERT: E 360 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8963 (tt) REVERT: F 46 TRP cc_start: 0.7866 (t-100) cc_final: 0.7550 (t-100) REVERT: F 115 ASP cc_start: 0.8298 (t70) cc_final: 0.7680 (t0) REVERT: F 303 ARG cc_start: 0.8014 (tpt170) cc_final: 0.7490 (mmt180) REVERT: F 360 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8965 (tt) REVERT: G 46 TRP cc_start: 0.7869 (t-100) cc_final: 0.7550 (t-100) REVERT: G 115 ASP cc_start: 0.8296 (t70) cc_final: 0.7680 (t0) REVERT: G 303 ARG cc_start: 0.8006 (tpt170) cc_final: 0.7481 (mmt180) REVERT: G 360 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8962 (tt) REVERT: H 46 TRP cc_start: 0.7872 (t-100) cc_final: 0.7555 (t-100) REVERT: H 115 ASP cc_start: 0.8296 (t70) cc_final: 0.7683 (t0) REVERT: H 303 ARG cc_start: 0.8016 (tpt170) cc_final: 0.7488 (mmt180) REVERT: H 360 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8962 (tt) outliers start: 59 outliers final: 11 residues processed: 440 average time/residue: 1.3556 time to fit residues: 680.9519 Evaluate side-chains 425 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 406 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 325 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 262 ASN Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 278 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 224 ASN A 261 ASN B 179 GLN B 224 ASN B 261 ASN C 179 GLN C 224 ASN C 261 ASN D 179 GLN D 224 ASN D 261 ASN E 179 GLN E 224 ASN E 261 ASN F 179 GLN F 224 ASN F 261 ASN G 179 GLN G 224 ASN G 261 ASN H 179 GLN H 224 ASN H 261 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23584 Z= 0.168 Angle : 0.518 5.233 31840 Z= 0.285 Chirality : 0.043 0.134 3416 Planarity : 0.003 0.033 4240 Dihedral : 4.817 28.162 3392 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.46 % Allowed : 12.46 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2968 helix: 0.99 (0.13), residues: 1480 sheet: -0.81 (0.24), residues: 456 loop : -1.74 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 46 HIS 0.005 0.001 HIS F 269 PHE 0.010 0.001 PHE D 99 TYR 0.017 0.001 TYR G 314 ARG 0.002 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 422 time to evaluate : 2.327 Fit side-chains REVERT: A 46 TRP cc_start: 0.7801 (t-100) cc_final: 0.7474 (t-100) REVERT: A 115 ASP cc_start: 0.8228 (t70) cc_final: 0.7954 (t0) REVERT: A 155 TYR cc_start: 0.8242 (t80) cc_final: 0.8022 (t80) REVERT: A 159 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7055 (mmmm) REVERT: A 303 ARG cc_start: 0.7960 (tpt170) cc_final: 0.7506 (mmt180) REVERT: A 355 GLN cc_start: 0.9121 (pt0) cc_final: 0.8915 (pt0) REVERT: A 360 ILE cc_start: 0.9115 (tp) cc_final: 0.8894 (tt) REVERT: B 46 TRP cc_start: 0.7829 (t-100) cc_final: 0.7510 (t-100) REVERT: B 115 ASP cc_start: 0.8232 (t70) cc_final: 0.7959 (t0) REVERT: B 155 TYR cc_start: 0.8246 (t80) cc_final: 0.8027 (t80) REVERT: B 159 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7046 (mmmm) REVERT: B 303 ARG cc_start: 0.7968 (tpt170) cc_final: 0.7511 (mmt180) REVERT: B 355 GLN cc_start: 0.9119 (pt0) cc_final: 0.8918 (pt0) REVERT: B 360 ILE cc_start: 0.9116 (tp) cc_final: 0.8897 (tt) REVERT: C 46 TRP cc_start: 0.7804 (t-100) cc_final: 0.7476 (t-100) REVERT: C 115 ASP cc_start: 0.8230 (t70) cc_final: 0.7953 (t0) REVERT: C 155 TYR cc_start: 0.8246 (t80) cc_final: 0.8025 (t80) REVERT: C 159 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7063 (mmmm) REVERT: C 303 ARG cc_start: 0.7958 (tpt170) cc_final: 0.7509 (mmt180) REVERT: C 355 GLN cc_start: 0.9119 (pt0) cc_final: 0.8910 (pt0) REVERT: C 360 ILE cc_start: 0.9116 (tp) cc_final: 0.8895 (tt) REVERT: D 46 TRP cc_start: 0.7805 (t-100) cc_final: 0.7476 (t-100) REVERT: D 115 ASP cc_start: 0.8236 (t70) cc_final: 0.7960 (t0) REVERT: D 155 TYR cc_start: 0.8250 (t80) cc_final: 0.8030 (t80) REVERT: D 159 LYS cc_start: 0.7527 (mmtm) cc_final: 0.7045 (mmmm) REVERT: D 303 ARG cc_start: 0.7965 (tpt170) cc_final: 0.7511 (mmt180) REVERT: D 360 ILE cc_start: 0.9118 (tp) cc_final: 0.8900 (tt) REVERT: E 46 TRP cc_start: 0.7801 (t-100) cc_final: 0.7472 (t-100) REVERT: E 115 ASP cc_start: 0.8234 (t70) cc_final: 0.7959 (t0) REVERT: E 155 TYR cc_start: 0.8245 (t80) cc_final: 0.8025 (t80) REVERT: E 159 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7049 (mmmm) REVERT: E 303 ARG cc_start: 0.7961 (tpt170) cc_final: 0.7511 (mmt180) REVERT: E 355 GLN cc_start: 0.9114 (pt0) cc_final: 0.8910 (pt0) REVERT: E 360 ILE cc_start: 0.9122 (tp) cc_final: 0.8905 (tt) REVERT: F 46 TRP cc_start: 0.7799 (t-100) cc_final: 0.7474 (t-100) REVERT: F 115 ASP cc_start: 0.8232 (t70) cc_final: 0.7956 (t0) REVERT: F 155 TYR cc_start: 0.8251 (t80) cc_final: 0.8035 (t80) REVERT: F 159 LYS cc_start: 0.7520 (mmtm) cc_final: 0.7056 (mmmm) REVERT: F 303 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7515 (mmt180) REVERT: F 360 ILE cc_start: 0.9120 (tp) cc_final: 0.8900 (tt) REVERT: G 46 TRP cc_start: 0.7801 (t-100) cc_final: 0.7472 (t-100) REVERT: G 115 ASP cc_start: 0.8231 (t70) cc_final: 0.7952 (t0) REVERT: G 155 TYR cc_start: 0.8241 (t80) cc_final: 0.8024 (t80) REVERT: G 159 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7060 (mmmm) REVERT: G 303 ARG cc_start: 0.7956 (tpt170) cc_final: 0.7503 (mmt180) REVERT: G 355 GLN cc_start: 0.9113 (pt0) cc_final: 0.8912 (pt0) REVERT: G 360 ILE cc_start: 0.9118 (tp) cc_final: 0.8898 (tt) REVERT: H 46 TRP cc_start: 0.7806 (t-100) cc_final: 0.7476 (t-100) REVERT: H 115 ASP cc_start: 0.8229 (t70) cc_final: 0.7953 (t0) REVERT: H 155 TYR cc_start: 0.8246 (t80) cc_final: 0.8028 (t80) REVERT: H 159 LYS cc_start: 0.7526 (mmtm) cc_final: 0.7043 (mmmm) REVERT: H 303 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7514 (mmt180) REVERT: H 355 GLN cc_start: 0.9121 (pt0) cc_final: 0.8919 (pt0) REVERT: H 360 ILE cc_start: 0.9115 (tp) cc_final: 0.8895 (tt) outliers start: 66 outliers final: 8 residues processed: 454 average time/residue: 1.2707 time to fit residues: 663.4396 Evaluate side-chains 416 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 408 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 224 ASN A 261 ASN B 179 GLN B 224 ASN B 261 ASN C 179 GLN C 224 ASN C 261 ASN D 179 GLN D 224 ASN D 261 ASN E 179 GLN E 224 ASN E 261 ASN F 179 GLN F 224 ASN G 179 GLN G 224 ASN G 261 ASN H 179 GLN H 224 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 23584 Z= 0.546 Angle : 0.693 6.892 31840 Z= 0.367 Chirality : 0.050 0.150 3416 Planarity : 0.007 0.056 4240 Dihedral : 5.201 27.317 3392 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.35 % Allowed : 12.29 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2968 helix: 0.84 (0.13), residues: 1480 sheet: -0.90 (0.24), residues: 456 loop : -1.69 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 46 HIS 0.006 0.002 HIS D 359 PHE 0.016 0.003 PHE A 4 TYR 0.022 0.003 TYR G 284 ARG 0.011 0.001 ARG H 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 428 time to evaluate : 2.242 Fit side-chains REVERT: A 16 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8529 (tt) REVERT: A 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7544 (t-100) REVERT: A 303 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7589 (mmt180) REVERT: B 16 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7546 (t-100) REVERT: B 303 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7593 (mmt180) REVERT: B 360 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8957 (tt) REVERT: C 16 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7545 (t-100) REVERT: C 303 ARG cc_start: 0.8037 (tpt170) cc_final: 0.7588 (mmt180) REVERT: C 360 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8942 (tt) REVERT: D 16 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8531 (tt) REVERT: D 46 TRP cc_start: 0.7818 (t-100) cc_final: 0.7546 (t-100) REVERT: D 303 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7596 (mmt180) REVERT: D 360 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8959 (tt) REVERT: E 16 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8541 (tt) REVERT: E 46 TRP cc_start: 0.7815 (t-100) cc_final: 0.7541 (t-100) REVERT: E 303 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7591 (mmt180) REVERT: F 16 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8534 (tt) REVERT: F 46 TRP cc_start: 0.7812 (t-100) cc_final: 0.7544 (t-100) REVERT: F 303 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7597 (mmt180) REVERT: G 16 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8554 (tt) REVERT: G 46 TRP cc_start: 0.7817 (t-100) cc_final: 0.7545 (t-100) REVERT: G 303 ARG cc_start: 0.8039 (tpt170) cc_final: 0.7586 (mmt180) REVERT: H 16 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8547 (tt) REVERT: H 46 TRP cc_start: 0.7818 (t-100) cc_final: 0.7546 (t-100) REVERT: H 303 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7591 (mmt180) outliers start: 87 outliers final: 14 residues processed: 461 average time/residue: 1.3378 time to fit residues: 704.8332 Evaluate side-chains 429 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 404 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 261 ASN B 179 GLN B 261 ASN C 179 GLN C 261 ASN D 179 GLN D 261 ASN E 179 GLN E 261 ASN F 179 GLN F 261 ASN G 179 GLN G 261 ASN H 179 GLN H 261 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23584 Z= 0.420 Angle : 0.628 6.632 31840 Z= 0.336 Chirality : 0.048 0.146 3416 Planarity : 0.005 0.043 4240 Dihedral : 5.069 27.264 3392 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.93 % Allowed : 15.96 % Favored : 80.11 % 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: -0.43 (0.15), residues: 2968 helix: 0.87 (0.13), residues: 1480 sheet: -0.88 (0.24), residues: 456 loop : -1.65 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 46 HIS 0.005 0.001 HIS B 359 PHE 0.009 0.002 PHE C 4 TYR 0.020 0.002 TYR G 314 ARG 0.008 0.001 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 403 time to evaluate : 2.833 Fit side-chains REVERT: A 16 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 46 TRP cc_start: 0.7807 (t-100) cc_final: 0.7526 (t-100) REVERT: A 303 ARG cc_start: 0.8043 (tpt170) cc_final: 0.7564 (mmt180) REVERT: B 16 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8522 (tt) REVERT: B 46 TRP cc_start: 0.7811 (t-100) cc_final: 0.7526 (t-100) REVERT: B 303 ARG cc_start: 0.8075 (tpt170) cc_final: 0.7607 (mmt180) REVERT: C 16 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 46 TRP cc_start: 0.7810 (t-100) cc_final: 0.7527 (t-100) REVERT: C 303 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7564 (mmt180) REVERT: D 16 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8541 (tt) REVERT: D 46 TRP cc_start: 0.7809 (t-100) cc_final: 0.7525 (t-100) REVERT: D 303 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7605 (mmt180) REVERT: E 16 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8519 (tt) REVERT: E 46 TRP cc_start: 0.7806 (t-100) cc_final: 0.7524 (t-100) REVERT: E 303 ARG cc_start: 0.8064 (tpt170) cc_final: 0.7602 (mmt180) REVERT: F 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8525 (tt) REVERT: F 46 TRP cc_start: 0.7806 (t-100) cc_final: 0.7524 (t-100) REVERT: F 303 ARG cc_start: 0.8075 (tpt170) cc_final: 0.7606 (mmt180) REVERT: G 16 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8520 (tt) REVERT: G 46 TRP cc_start: 0.7809 (t-100) cc_final: 0.7526 (t-100) REVERT: G 303 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7565 (mmt180) REVERT: H 16 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8523 (tt) REVERT: H 46 TRP cc_start: 0.7811 (t-100) cc_final: 0.7528 (t-100) REVERT: H 303 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7569 (mmt180) outliers start: 77 outliers final: 26 residues processed: 430 average time/residue: 1.3722 time to fit residues: 673.4205 Evaluate side-chains 437 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 403 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 325 LYS Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 262 ASN Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 0.0870 chunk 234 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 224 ASN B 179 GLN B 224 ASN B 302 ASN C 179 GLN C 224 ASN D 179 GLN D 224 ASN E 179 GLN E 224 ASN F 179 GLN F 224 ASN G 179 GLN G 224 ASN H 179 GLN H 224 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 23584 Z= 0.334 Angle : 0.583 6.309 31840 Z= 0.313 Chirality : 0.046 0.144 3416 Planarity : 0.004 0.036 4240 Dihedral : 4.939 28.701 3392 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.97 % Allowed : 15.96 % Favored : 80.07 % 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: -0.23 (0.15), residues: 2968 helix: 1.04 (0.13), residues: 1480 sheet: -0.72 (0.24), residues: 456 loop : -1.59 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP B 46 HIS 0.005 0.001 HIS H 269 PHE 0.008 0.002 PHE D 99 TYR 0.024 0.002 TYR A 155 ARG 0.005 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 389 time to evaluate : 2.479 Fit side-chains REVERT: A 16 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 46 TRP cc_start: 0.7795 (t-100) cc_final: 0.7536 (t-100) REVERT: A 303 ARG cc_start: 0.7993 (tpt170) cc_final: 0.7603 (mmt180) REVERT: A 355 GLN cc_start: 0.9194 (pt0) cc_final: 0.8982 (pt0) REVERT: B 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8523 (tt) REVERT: B 46 TRP cc_start: 0.7800 (t-100) cc_final: 0.7501 (t-100) REVERT: B 303 ARG cc_start: 0.8028 (tpt170) cc_final: 0.7647 (mmt180) REVERT: C 16 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8520 (tt) REVERT: C 46 TRP cc_start: 0.7798 (t-100) cc_final: 0.7501 (t-100) REVERT: C 303 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7607 (mmt180) REVERT: D 16 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8524 (tt) REVERT: D 46 TRP cc_start: 0.7795 (t-100) cc_final: 0.7499 (t-100) REVERT: D 303 ARG cc_start: 0.8028 (tpt170) cc_final: 0.7645 (mmt180) REVERT: E 16 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8519 (tt) REVERT: E 46 TRP cc_start: 0.7795 (t-100) cc_final: 0.7497 (t-100) REVERT: E 303 ARG cc_start: 0.8023 (tpt170) cc_final: 0.7648 (mmt180) REVERT: F 16 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8524 (tt) REVERT: F 46 TRP cc_start: 0.7793 (t-100) cc_final: 0.7497 (t-100) REVERT: F 303 ARG cc_start: 0.8028 (tpt170) cc_final: 0.7651 (mmt180) REVERT: G 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8520 (tt) REVERT: G 46 TRP cc_start: 0.7795 (t-100) cc_final: 0.7500 (t-100) REVERT: G 303 ARG cc_start: 0.7993 (tpt170) cc_final: 0.7605 (mmt180) REVERT: G 355 GLN cc_start: 0.9188 (pt0) cc_final: 0.8983 (pt0) REVERT: H 16 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8521 (tt) REVERT: H 46 TRP cc_start: 0.7800 (t-100) cc_final: 0.7536 (t-100) REVERT: H 303 ARG cc_start: 0.7997 (tpt170) cc_final: 0.7617 (mmt180) outliers start: 78 outliers final: 25 residues processed: 424 average time/residue: 1.3308 time to fit residues: 645.8455 Evaluate side-chains 429 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 396 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 262 ASN Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 179 GLN B 302 ASN C 179 GLN D 179 GLN E 179 GLN F 179 GLN G 179 GLN H 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23584 Z= 0.224 Angle : 0.532 5.591 31840 Z= 0.288 Chirality : 0.044 0.141 3416 Planarity : 0.003 0.031 4240 Dihedral : 4.697 27.468 3392 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.58 % Allowed : 17.36 % Favored : 80.07 % 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: -0.01 (0.15), residues: 2968 helix: 1.24 (0.13), residues: 1480 sheet: -0.61 (0.24), residues: 456 loop : -1.54 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 46 HIS 0.005 0.001 HIS F 269 PHE 0.008 0.002 PHE E 99 TYR 0.020 0.002 TYR G 155 ARG 0.002 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 395 time to evaluate : 2.507 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 16 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 46 TRP cc_start: 0.7780 (t-100) cc_final: 0.7506 (t-100) REVERT: A 303 ARG cc_start: 0.8016 (tpt170) cc_final: 0.7654 (mmt180) REVERT: A 355 GLN cc_start: 0.9162 (pt0) cc_final: 0.8924 (pt0) REVERT: B 16 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 46 TRP cc_start: 0.7781 (t-100) cc_final: 0.7503 (t-100) REVERT: B 303 ARG cc_start: 0.8066 (tpt170) cc_final: 0.7622 (mmt180) REVERT: C 16 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8450 (tt) REVERT: C 46 TRP cc_start: 0.7779 (t-100) cc_final: 0.7504 (t-100) REVERT: C 303 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7621 (mmt180) REVERT: D 16 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8454 (tt) REVERT: D 46 TRP cc_start: 0.7778 (t-100) cc_final: 0.7503 (t-100) REVERT: D 303 ARG cc_start: 0.8063 (tpt170) cc_final: 0.7619 (mmt180) REVERT: E 16 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8451 (tt) REVERT: E 46 TRP cc_start: 0.7776 (t-100) cc_final: 0.7502 (t-100) REVERT: E 303 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7618 (mmt180) REVERT: F 16 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8450 (tt) REVERT: F 46 TRP cc_start: 0.7774 (t-100) cc_final: 0.7500 (t-100) REVERT: F 303 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7622 (mmt180) REVERT: G 16 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8453 (tt) REVERT: G 46 TRP cc_start: 0.7778 (t-100) cc_final: 0.7501 (t-100) REVERT: G 303 ARG cc_start: 0.8061 (tpt170) cc_final: 0.7622 (mmt180) REVERT: G 355 GLN cc_start: 0.9158 (pt0) cc_final: 0.8924 (pt0) REVERT: H 16 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8454 (tt) REVERT: H 46 TRP cc_start: 0.7783 (t-100) cc_final: 0.7507 (t-100) REVERT: H 303 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7660 (mmt180) outliers start: 45 outliers final: 20 residues processed: 415 average time/residue: 1.3395 time to fit residues: 641.0134 Evaluate side-chains 409 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 381 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 0.0870 chunk 112 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 224 ASN B 179 GLN B 224 ASN B 302 ASN C 179 GLN C 224 ASN D 179 GLN D 224 ASN E 179 GLN E 224 ASN F 179 GLN F 224 ASN G 179 GLN G 224 ASN H 179 GLN H 224 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23584 Z= 0.352 Angle : 0.587 6.438 31840 Z= 0.314 Chirality : 0.046 0.141 3416 Planarity : 0.005 0.040 4240 Dihedral : 4.845 27.789 3392 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.91 % Allowed : 17.23 % Favored : 79.86 % 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: -0.05 (0.15), residues: 2968 helix: 1.17 (0.13), residues: 1480 sheet: -0.57 (0.24), residues: 456 loop : -1.51 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 46 HIS 0.004 0.001 HIS B 269 PHE 0.011 0.002 PHE B 166 TYR 0.024 0.002 TYR A 155 ARG 0.005 0.001 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 381 time to evaluate : 2.399 Fit side-chains REVERT: A 16 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8526 (tt) REVERT: A 46 TRP cc_start: 0.7743 (t-100) cc_final: 0.7469 (t-100) REVERT: A 303 ARG cc_start: 0.8070 (tpt170) cc_final: 0.7695 (mmt180) REVERT: A 355 GLN cc_start: 0.9214 (pt0) cc_final: 0.9012 (pt0) REVERT: B 16 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 46 TRP cc_start: 0.7747 (t-100) cc_final: 0.7471 (t-100) REVERT: B 303 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7696 (mmt180) REVERT: C 16 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8524 (tt) REVERT: C 46 TRP cc_start: 0.7744 (t-100) cc_final: 0.7473 (t-100) REVERT: C 303 ARG cc_start: 0.8083 (tpt170) cc_final: 0.7703 (mmt180) REVERT: D 16 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8530 (tt) REVERT: D 46 TRP cc_start: 0.7744 (t-100) cc_final: 0.7473 (t-100) REVERT: D 303 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7699 (mmt180) REVERT: E 16 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8525 (tt) REVERT: E 46 TRP cc_start: 0.7758 (t-100) cc_final: 0.7491 (t-100) REVERT: E 303 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7706 (mmt180) REVERT: F 16 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8528 (tt) REVERT: F 46 TRP cc_start: 0.7740 (t-100) cc_final: 0.7469 (t-100) REVERT: F 303 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7706 (mmt180) REVERT: G 16 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8526 (tt) REVERT: G 46 TRP cc_start: 0.7759 (t-100) cc_final: 0.7490 (t-100) REVERT: G 303 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7707 (mmt180) REVERT: H 16 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8526 (tt) REVERT: H 46 TRP cc_start: 0.7749 (t-100) cc_final: 0.7476 (t-100) REVERT: H 303 ARG cc_start: 0.8079 (tpt170) cc_final: 0.7699 (mmt180) outliers start: 53 outliers final: 21 residues processed: 399 average time/residue: 1.2956 time to fit residues: 591.5415 Evaluate side-chains 409 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 380 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 0.0370 chunk 176 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 302 ASN B 179 GLN B 302 ASN C 179 GLN D 179 GLN E 179 GLN F 179 GLN G 179 GLN G 302 ASN H 179 GLN H 261 ASN H 302 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23584 Z= 0.174 Angle : 0.506 5.306 31840 Z= 0.274 Chirality : 0.043 0.142 3416 Planarity : 0.003 0.030 4240 Dihedral : 4.497 26.178 3392 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.24 % Allowed : 17.44 % Favored : 80.32 % 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: 0.24 (0.15), residues: 2968 helix: 1.41 (0.13), residues: 1480 sheet: -0.33 (0.24), residues: 456 loop : -1.44 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 46 HIS 0.005 0.001 HIS F 269 PHE 0.009 0.002 PHE B 166 TYR 0.020 0.002 TYR A 155 ARG 0.002 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 379 time to evaluate : 2.594 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: A 16 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 46 TRP cc_start: 0.7758 (t-100) cc_final: 0.7471 (t-100) REVERT: A 303 ARG cc_start: 0.7963 (tpt170) cc_final: 0.7624 (mmt180) REVERT: A 355 GLN cc_start: 0.9100 (pt0) cc_final: 0.8859 (pt0) REVERT: B 16 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 46 TRP cc_start: 0.7779 (t-100) cc_final: 0.7488 (t-100) REVERT: B 303 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7612 (mmt180) REVERT: C 16 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 46 TRP cc_start: 0.7778 (t-100) cc_final: 0.7492 (t-100) REVERT: C 303 ARG cc_start: 0.8004 (tpt170) cc_final: 0.7655 (mmt180) REVERT: D 16 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8417 (tt) REVERT: D 46 TRP cc_start: 0.7776 (t-100) cc_final: 0.7488 (t-100) REVERT: D 303 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7617 (mmt180) REVERT: E 16 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8411 (tt) REVERT: E 46 TRP cc_start: 0.7775 (t-100) cc_final: 0.7490 (t-100) REVERT: E 303 ARG cc_start: 0.7969 (tpt170) cc_final: 0.7621 (mmt180) REVERT: F 16 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8389 (tt) REVERT: F 46 TRP cc_start: 0.7771 (t-100) cc_final: 0.7485 (t-100) REVERT: F 303 ARG cc_start: 0.7974 (tpt170) cc_final: 0.7625 (mmt180) REVERT: G 16 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8412 (tt) REVERT: G 46 TRP cc_start: 0.7773 (t-100) cc_final: 0.7485 (t-100) REVERT: G 303 ARG cc_start: 0.7940 (tpt170) cc_final: 0.7589 (mmt180) REVERT: H 16 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8416 (tt) REVERT: H 46 TRP cc_start: 0.7777 (t-100) cc_final: 0.7486 (t-100) REVERT: H 303 ARG cc_start: 0.7928 (tpt170) cc_final: 0.7578 (mmt180) outliers start: 37 outliers final: 20 residues processed: 400 average time/residue: 1.4548 time to fit residues: 671.9347 Evaluate side-chains 403 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 375 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 362 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 362 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 325 LYS Chi-restraints excluded: chain H residue 329 ILE Chi-restraints excluded: chain H residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 4.9990 chunk 243 optimal weight: 0.2980 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 224 ASN A 302 ASN B 179 GLN B 224 ASN B 302 ASN C 179 GLN C 224 ASN D 179 GLN D 224 ASN E 179 GLN E 224 ASN F 179 GLN F 224 ASN G 179 GLN G 224 ASN G 302 ASN H 179 GLN H 224 ASN H 302 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.187692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144277 restraints weight = 111344.933| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 6.23 r_work: 0.2747 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23584 Z= 0.245 Angle : 0.534 6.029 31840 Z= 0.286 Chirality : 0.044 0.142 3416 Planarity : 0.004 0.028 4240 Dihedral : 4.576 27.576 3392 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.15 % Allowed : 18.24 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 2968 helix: 1.44 (0.13), residues: 1480 sheet: -0.28 (0.24), residues: 456 loop : -1.45 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 46 HIS 0.004 0.001 HIS H 269 PHE 0.012 0.002 PHE E 166 TYR 0.023 0.002 TYR B 155 ARG 0.003 0.001 ARG A 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9762.66 seconds wall clock time: 173 minutes 35.28 seconds (10415.28 seconds total)