Starting phenix.real_space_refine on Fri Feb 16 14:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/02_2024/8br2_16197_updated.pdb" } resolution = 2.9 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 58 5.49 5 S 78 5.16 5 C 9477 2.51 5 N 2757 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ASP 336": "OD1" <-> "OD2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E ASP 336": "OD1" <-> "OD2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F ASP 336": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15574 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "B" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "C" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "D" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "E" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "F" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 residue: pdb=" N AARG A 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 254 " occ=0.50 residue: pdb=" N AARG B 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 130 " occ=0.50 residue: pdb=" N AARG B 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 254 " occ=0.50 residue: pdb=" N AARG C 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 130 " occ=0.50 residue: pdb=" N AARG C 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 254 " occ=0.50 residue: pdb=" N AARG D 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 130 " occ=0.50 residue: pdb=" N AARG D 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 254 " occ=0.50 residue: pdb=" N AARG E 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 130 " occ=0.50 residue: pdb=" N AARG E 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 254 " occ=0.50 residue: pdb=" N AARG F 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 130 " occ=0.50 residue: pdb=" N AARG F 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 254 " occ=0.50 Time building chain proxies: 15.73, per 1000 atoms: 1.01 Number of scatterers: 15574 At special positions: 0 Unit cell: (126.488, 138.224, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 78 16.00 P 58 15.00 O 3192 8.00 N 2757 7.00 C 9477 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: 7.19 Conformation dependent library (CDL) restraints added in 5.4 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 12 sheets defined 45.7% alpha, 16.1% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 7.10 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.552A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.590A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.885A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.099A pdb=" N ASP A 231 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 259 removed outlier: 5.139A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 240 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 258 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.515A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.552A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.590A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.884A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 4.098A pdb=" N ASP B 231 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 259 removed outlier: 5.140A pdb=" N SER B 239 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 240 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 252 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.516A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.553A pdb=" N ALA C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.590A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.885A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 4.098A pdb=" N ASP C 231 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 259 removed outlier: 5.140A pdb=" N SER C 239 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 240 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 245 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 252 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 258 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.516A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.553A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.590A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 197 through 213 removed outlier: 3.884A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 removed outlier: 4.098A pdb=" N ASP D 231 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 259 removed outlier: 5.139A pdb=" N SER D 239 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 240 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 245 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 259 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.516A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.552A pdb=" N ALA E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.589A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 197 through 213 removed outlier: 3.885A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 4.098A pdb=" N ASP E 231 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 259 removed outlier: 5.140A pdb=" N SER E 239 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 240 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 245 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 252 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU E 258 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE E 259 " --> pdb=" O ALA E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.516A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 35 through 44 removed outlier: 3.552A pdb=" N ALA F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.531A pdb=" N LYS F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 133 through 145 removed outlier: 3.590A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 197 through 213 removed outlier: 3.885A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 231 removed outlier: 4.098A pdb=" N ASP F 231 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 259 removed outlier: 5.140A pdb=" N SER F 239 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 240 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 245 " --> pdb=" O GLN F 242 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 252 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU F 258 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE F 259 " --> pdb=" O ALA F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.516A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 263 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET A 125 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 265 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY A 127 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 267 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= C, first strand: chain 'B' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 263 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N MET B 125 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 265 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY B 127 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 267 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= E, first strand: chain 'C' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 263 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET C 125 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 265 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY C 127 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C 267 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS C 156 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 219 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET C 158 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL C 221 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 160 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 269 through 271 Processing sheet with id= G, first strand: chain 'D' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 263 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET D 125 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 265 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY D 127 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN D 267 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS D 156 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU D 219 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET D 158 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL D 221 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE D 160 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 269 through 271 Processing sheet with id= I, first strand: chain 'E' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL E 263 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N MET E 125 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 265 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY E 127 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN E 267 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL E 221 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE E 160 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 269 through 271 Processing sheet with id= K, first strand: chain 'F' and resid 333 through 335 removed outlier: 5.915A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL F 263 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N MET F 125 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 265 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY F 127 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN F 267 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS F 156 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 219 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET F 158 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL F 221 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE F 160 " --> pdb=" O VAL F 221 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 269 through 271 582 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2549 1.31 - 1.43: 4095 1.43 - 1.56: 8890 1.56 - 1.68: 108 1.68 - 1.80: 126 Bond restraints: 15768 Sorted by residual: bond pdb=" C5 DA H 20 " pdb=" C6 DA H 20 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" N1 DT H 17 " pdb=" C6 DT H 17 " ideal model delta sigma weight residual 1.380 1.460 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" N9 DA H 14 " pdb=" C8 DA H 14 " ideal model delta sigma weight residual 1.367 1.446 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " ideal model delta sigma weight residual 1.364 1.440 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" SD MET D 251 " pdb=" CE MET D 251 " ideal model delta sigma weight residual 1.791 1.706 0.085 2.50e-02 1.60e+03 1.16e+01 ... (remaining 15763 not shown) Histogram of bond angle deviations from ideal: 100.12 - 108.01: 895 108.01 - 115.91: 9717 115.91 - 123.80: 10420 123.80 - 131.70: 431 131.70 - 139.59: 25 Bond angle restraints: 21488 Sorted by residual: angle pdb=" CA BARG F 130 " pdb=" CB BARG F 130 " pdb=" CG BARG F 130 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA BARG C 130 " pdb=" CB BARG C 130 " pdb=" CG BARG C 130 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG E 130 " pdb=" CB BARG E 130 " pdb=" CG BARG E 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG D 130 " pdb=" CB BARG D 130 " pdb=" CG BARG D 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG A 130 " pdb=" CB BARG A 130 " pdb=" CG BARG A 130 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8212 17.90 - 35.81: 967 35.81 - 53.71: 272 53.71 - 71.61: 101 71.61 - 89.51: 38 Dihedral angle restraints: 9590 sinusoidal: 4220 harmonic: 5370 Sorted by residual: dihedral pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CD ARG E 303 " pdb=" NE ARG E 303 " pdb=" CZ ARG E 303 " pdb=" NH1 ARG E 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CD ARG C 303 " pdb=" NE ARG C 303 " pdb=" CZ ARG C 303 " pdb=" NH1 ARG C 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 9587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1418 0.033 - 0.066: 715 0.066 - 0.099: 201 0.099 - 0.132: 87 0.132 - 0.165: 13 Chirality restraints: 2434 Sorted by residual: chirality pdb=" CA BARG A 130 " pdb=" N BARG A 130 " pdb=" C BARG A 130 " pdb=" CB BARG A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA BARG C 130 " pdb=" N BARG C 130 " pdb=" C BARG C 130 " pdb=" CB BARG C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA BARG E 130 " pdb=" N BARG E 130 " pdb=" C BARG E 130 " pdb=" CB BARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 2431 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 303 " -1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 303 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 303 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 303 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG B 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 303 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG F 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG F 303 " 0.016 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 480 2.67 - 3.23: 14794 3.23 - 3.79: 24976 3.79 - 4.34: 37816 4.34 - 4.90: 58026 Nonbonded interactions: 136092 Sorted by model distance: nonbonded pdb=" OG1 THR F 134 " pdb="CA CA F 401 " model vdw 2.117 2.510 nonbonded pdb=" OG1 THR A 134 " pdb="CA CA A 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR E 134 " pdb="CA CA E 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR B 134 " pdb="CA CA B 401 " model vdw 2.118 2.510 ... (remaining 136087 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 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'B' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'C' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'D' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'E' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'F' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) } 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=0.99 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: 0.570 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: 2.830 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 59.650 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 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:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.085 15768 Z= 0.498 Angle : 0.556 6.377 21488 Z= 0.311 Chirality : 0.045 0.165 2434 Planarity : 0.024 0.490 2632 Dihedral : 18.028 89.513 6158 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.80 % Allowed : 22.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.17), residues: 1878 helix: -2.43 (0.13), residues: 894 sheet: 0.23 (0.30), residues: 306 loop : -1.87 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 294 PHE 0.008 0.002 PHE D 129 TYR 0.010 0.002 TYR A 159 ARG 0.005 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 444 time to evaluate : 1.799 Fit side-chains REVERT: A 176 GLU cc_start: 0.7387 (tp30) cc_final: 0.7038 (tp30) REVERT: A 243 MET cc_start: 0.8725 (mtp) cc_final: 0.8365 (mtt) REVERT: A 266 THR cc_start: 0.8968 (m) cc_final: 0.8599 (m) REVERT: A 268 GLN cc_start: 0.9032 (mt0) cc_final: 0.8641 (mt0) REVERT: B 40 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7272 (mttt) REVERT: B 95 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7879 (mtm110) REVERT: B 187 ASP cc_start: 0.8264 (m-30) cc_final: 0.7922 (m-30) REVERT: C 39 LYS cc_start: 0.8098 (mttt) cc_final: 0.7682 (ttpt) REVERT: C 70 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6555 (mmmm) REVERT: C 176 GLU cc_start: 0.7955 (tp30) cc_final: 0.7551 (tp30) REVERT: C 205 TYR cc_start: 0.8273 (m-80) cc_final: 0.8024 (m-80) REVERT: C 235 ARG cc_start: 0.9057 (ttp-170) cc_final: 0.8533 (ttp-170) REVERT: D 43 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7339 (mm-30) REVERT: D 108 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7637 (tp30) REVERT: D 111 LYS cc_start: 0.8070 (mttp) cc_final: 0.7812 (mtmt) REVERT: D 210 MET cc_start: 0.9015 (mtp) cc_final: 0.8798 (mtm) REVERT: E 40 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6882 (mmtp) REVERT: E 111 LYS cc_start: 0.7993 (mttp) cc_final: 0.7712 (mttt) REVERT: E 200 GLN cc_start: 0.9231 (tt0) cc_final: 0.8999 (tt0) REVERT: E 284 LYS cc_start: 0.8046 (pttm) cc_final: 0.7673 (ptmt) REVERT: F 70 LYS cc_start: 0.5470 (mmtt) cc_final: 0.5072 (mmtt) REVERT: F 210 MET cc_start: 0.8417 (mtp) cc_final: 0.7983 (mtp) REVERT: F 330 ASN cc_start: 0.8432 (m-40) cc_final: 0.8216 (m110) outliers start: 6 outliers final: 5 residues processed: 450 average time/residue: 1.6358 time to fit residues: 792.7182 Evaluate side-chains 246 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain E residue 31 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 145 GLN B 202 GLN B 330 ASN C 23 GLN C 138 HIS C 145 GLN C 202 GLN C 206 GLN D 114 GLN D 145 GLN D 202 GLN E 206 GLN E 290 ASN F 202 GLN F 206 GLN F 290 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15768 Z= 0.225 Angle : 0.530 7.115 21488 Z= 0.290 Chirality : 0.040 0.152 2434 Planarity : 0.005 0.049 2632 Dihedral : 15.523 88.995 2707 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.72 % Allowed : 23.90 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.66 (0.18), residues: 1878 helix: -1.25 (0.15), residues: 900 sheet: 0.11 (0.29), residues: 336 loop : -1.26 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 93 PHE 0.015 0.002 PHE F 46 TYR 0.015 0.001 TYR B 159 ARG 0.006 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7167 (mttp) REVERT: A 107 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8223 (mtpt) REVERT: A 206 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 266 THR cc_start: 0.9047 (m) cc_final: 0.8814 (m) REVERT: B 94 GLN cc_start: 0.7903 (mt0) cc_final: 0.7653 (mt0) REVERT: B 161 ASP cc_start: 0.8677 (t70) cc_final: 0.8476 (t70) REVERT: B 165 THR cc_start: 0.8342 (m) cc_final: 0.8052 (p) REVERT: B 210 MET cc_start: 0.8723 (mtp) cc_final: 0.8422 (mtp) REVERT: C 39 LYS cc_start: 0.7624 (mttt) cc_final: 0.7380 (ttpt) REVERT: C 70 LYS cc_start: 0.6793 (mmtt) cc_final: 0.6500 (mmmm) REVERT: C 176 GLU cc_start: 0.7951 (tp30) cc_final: 0.7459 (tp30) REVERT: C 205 TYR cc_start: 0.8354 (m-80) cc_final: 0.8067 (m-80) REVERT: D 43 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7064 (mp0) REVERT: D 111 LYS cc_start: 0.8158 (mttp) cc_final: 0.7731 (mtmt) REVERT: E 39 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7674 (ptmt) REVERT: E 40 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6996 (mmtp) REVERT: E 111 LYS cc_start: 0.7526 (mttp) cc_final: 0.7297 (mttt) REVERT: E 243 MET cc_start: 0.8328 (mtp) cc_final: 0.8091 (mtm) REVERT: F 108 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: F 210 MET cc_start: 0.8417 (mtp) cc_final: 0.8152 (mtp) REVERT: F 211 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8360 (mtt) outliers start: 41 outliers final: 11 residues processed: 285 average time/residue: 1.8716 time to fit residues: 571.2279 Evaluate side-chains 248 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 290 ASN B 202 GLN C 23 GLN C 202 GLN D 202 GLN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15768 Z= 0.318 Angle : 0.548 6.837 21488 Z= 0.295 Chirality : 0.042 0.134 2434 Planarity : 0.005 0.050 2632 Dihedral : 15.247 89.456 2705 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.19 % Allowed : 24.70 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.44 (0.18), residues: 1878 helix: -0.79 (0.16), residues: 894 sheet: -0.28 (0.31), residues: 270 loop : -1.23 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 93 PHE 0.015 0.002 PHE F 46 TYR 0.016 0.002 TYR B 159 ARG 0.004 0.001 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7166 (mttp) REVERT: A 107 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: A 206 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: A 326 MET cc_start: 0.8250 (ttp) cc_final: 0.7963 (mtp) REVERT: B 27 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6086 (ttt90) REVERT: B 30 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.5311 (mp10) REVERT: B 57 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7634 (tttt) REVERT: B 73 LYS cc_start: 0.7921 (tttp) cc_final: 0.7643 (ttpt) REVERT: B 161 ASP cc_start: 0.8706 (t70) cc_final: 0.8442 (t70) REVERT: B 165 THR cc_start: 0.8489 (m) cc_final: 0.8129 (p) REVERT: B 177 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8244 (ttt180) REVERT: B 326 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7917 (tmm) REVERT: C 39 LYS cc_start: 0.7680 (mttt) cc_final: 0.7440 (ttpt) REVERT: C 70 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6506 (mmmm) REVERT: C 176 GLU cc_start: 0.8027 (tp30) cc_final: 0.7573 (tp30) REVERT: C 205 TYR cc_start: 0.8376 (m-80) cc_final: 0.8079 (m-80) REVERT: C 306 ARG cc_start: 0.7317 (tmm160) cc_final: 0.6938 (tmm160) REVERT: D 43 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7118 (mp0) REVERT: D 111 LYS cc_start: 0.8323 (mttp) cc_final: 0.7782 (mtmt) REVERT: D 184 ASP cc_start: 0.7610 (m-30) cc_final: 0.7364 (m-30) REVERT: E 39 LYS cc_start: 0.8055 (mmmm) cc_final: 0.7684 (ptmt) REVERT: E 40 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7359 (mmtp) REVERT: E 80 LYS cc_start: 0.6947 (pptt) cc_final: 0.6741 (pptt) REVERT: E 111 LYS cc_start: 0.7892 (mttp) cc_final: 0.7529 (mttt) REVERT: F 42 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7562 (mt-10) REVERT: F 50 GLU cc_start: 0.8039 (mp0) cc_final: 0.7831 (mp0) REVERT: F 58 LYS cc_start: 0.7515 (mtpt) cc_final: 0.6925 (mtpt) REVERT: F 210 MET cc_start: 0.8436 (mtp) cc_final: 0.8111 (mtp) REVERT: F 215 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7868 (tmm160) outliers start: 42 outliers final: 17 residues processed: 267 average time/residue: 2.0193 time to fit residues: 575.8212 Evaluate side-chains 256 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 202 GLN C 23 GLN C 101 GLN C 202 GLN D 202 GLN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15768 Z= 0.221 Angle : 0.497 7.335 21488 Z= 0.268 Chirality : 0.040 0.118 2434 Planarity : 0.004 0.049 2632 Dihedral : 15.188 89.436 2703 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.72 % Allowed : 25.03 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.13 (0.19), residues: 1878 helix: -0.48 (0.17), residues: 888 sheet: -0.14 (0.32), residues: 264 loop : -1.15 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 244 PHE 0.013 0.002 PHE F 46 TYR 0.025 0.001 TYR F 178 ARG 0.006 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7157 (mttp) REVERT: A 107 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (mtpt) REVERT: A 326 MET cc_start: 0.8220 (ttp) cc_final: 0.7922 (mtp) REVERT: B 27 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6015 (tpt90) REVERT: B 30 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.5252 (mp10) REVERT: B 57 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7572 (tttt) REVERT: B 73 LYS cc_start: 0.7896 (tttp) cc_final: 0.7614 (ttpt) REVERT: B 161 ASP cc_start: 0.8677 (t70) cc_final: 0.8386 (t70) REVERT: B 165 THR cc_start: 0.8418 (m) cc_final: 0.8097 (p) REVERT: B 326 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7890 (tmm) REVERT: C 39 LYS cc_start: 0.7781 (mttt) cc_final: 0.7570 (ttpt) REVERT: C 176 GLU cc_start: 0.7991 (tp30) cc_final: 0.7558 (tp30) REVERT: C 205 TYR cc_start: 0.8374 (m-80) cc_final: 0.8078 (m-80) REVERT: D 43 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6897 (mp0) REVERT: D 111 LYS cc_start: 0.8334 (mttp) cc_final: 0.7830 (mtmt) REVERT: D 184 ASP cc_start: 0.7607 (m-30) cc_final: 0.7358 (m-30) REVERT: E 39 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7642 (ptmt) REVERT: E 40 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7351 (mmtp) REVERT: E 111 LYS cc_start: 0.7956 (mttp) cc_final: 0.7583 (mttt) REVERT: E 215 ARG cc_start: 0.8829 (ttt90) cc_final: 0.8564 (ttt90) REVERT: E 243 MET cc_start: 0.8286 (mtp) cc_final: 0.8067 (mtm) REVERT: F 42 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7487 (mt-10) REVERT: F 58 LYS cc_start: 0.7512 (mtpt) cc_final: 0.6928 (mtpt) REVERT: F 210 MET cc_start: 0.8484 (mtp) cc_final: 0.8132 (mtp) outliers start: 35 outliers final: 15 residues processed: 262 average time/residue: 1.8626 time to fit residues: 522.7400 Evaluate side-chains 246 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 0.0980 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN C 23 GLN C 202 GLN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15768 Z= 0.353 Angle : 0.565 8.836 21488 Z= 0.302 Chirality : 0.043 0.131 2434 Planarity : 0.005 0.048 2632 Dihedral : 15.183 89.310 2702 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.65 % Allowed : 24.44 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -1.20 (0.19), residues: 1878 helix: -0.62 (0.17), residues: 900 sheet: -0.16 (0.32), residues: 264 loop : -1.06 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 93 PHE 0.017 0.002 PHE A 92 TYR 0.015 0.002 TYR B 315 ARG 0.006 0.001 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 241 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7270 (mttp) REVERT: A 326 MET cc_start: 0.8251 (ttp) cc_final: 0.7939 (mtp) REVERT: B 27 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6323 (tpt90) REVERT: B 30 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.5334 (mp10) REVERT: B 57 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7680 (tttt) REVERT: B 73 LYS cc_start: 0.7987 (tttp) cc_final: 0.7687 (ttpt) REVERT: B 165 THR cc_start: 0.8458 (m) cc_final: 0.8231 (p) REVERT: B 326 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7893 (tmm) REVERT: C 39 LYS cc_start: 0.7849 (mttt) cc_final: 0.7528 (ttpt) REVERT: C 176 GLU cc_start: 0.8050 (tp30) cc_final: 0.7619 (tp30) REVERT: C 205 TYR cc_start: 0.8437 (m-80) cc_final: 0.8070 (m-80) REVERT: D 43 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6956 (mp0) REVERT: D 111 LYS cc_start: 0.8245 (mttp) cc_final: 0.7778 (mtmt) REVERT: D 177 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8386 (ttt-90) REVERT: E 39 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7684 (ptmt) REVERT: E 40 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7276 (mmtp) REVERT: E 111 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: E 158 MET cc_start: 0.8957 (ttm) cc_final: 0.8722 (ttp) REVERT: F 42 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7586 (mt-10) REVERT: F 210 MET cc_start: 0.8460 (mtp) cc_final: 0.8138 (mtp) REVERT: F 214 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8206 (t) REVERT: F 215 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8000 (tmm160) outliers start: 49 outliers final: 23 residues processed: 272 average time/residue: 1.9104 time to fit residues: 556.3320 Evaluate side-chains 264 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 215 ARG Chi-restraints excluded: chain F residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15768 Z= 0.159 Angle : 0.461 6.520 21488 Z= 0.250 Chirality : 0.038 0.122 2434 Planarity : 0.004 0.046 2632 Dihedral : 15.024 89.820 2702 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.99 % Allowed : 26.10 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.81 (0.19), residues: 1878 helix: -0.23 (0.17), residues: 888 sheet: 0.40 (0.37), residues: 210 loop : -1.03 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 93 PHE 0.011 0.001 PHE F 46 TYR 0.009 0.001 TYR D 232 ARG 0.006 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 326 MET cc_start: 0.8222 (ttp) cc_final: 0.7928 (mtp) REVERT: B 27 ARG cc_start: 0.7515 (mtp180) cc_final: 0.6229 (tpt90) REVERT: B 30 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.5238 (mp10) REVERT: B 57 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7474 (tttt) REVERT: B 73 LYS cc_start: 0.7976 (tttp) cc_final: 0.7649 (ttpt) REVERT: B 161 ASP cc_start: 0.8643 (t70) cc_final: 0.8362 (t70) REVERT: B 165 THR cc_start: 0.8373 (m) cc_final: 0.8085 (p) REVERT: C 176 GLU cc_start: 0.7854 (tp30) cc_final: 0.7414 (tp30) REVERT: C 205 TYR cc_start: 0.8414 (m-80) cc_final: 0.8118 (m-80) REVERT: D 43 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6872 (mp0) REVERT: D 73 LYS cc_start: 0.8531 (tttt) cc_final: 0.8319 (tttt) REVERT: D 111 LYS cc_start: 0.8250 (mttp) cc_final: 0.7769 (mtmt) REVERT: E 39 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7633 (ptmt) REVERT: E 40 LYS cc_start: 0.7502 (mmtt) cc_final: 0.7258 (mmtp) REVERT: E 111 LYS cc_start: 0.7937 (mttp) cc_final: 0.7543 (mttt) REVERT: E 158 MET cc_start: 0.8946 (ttm) cc_final: 0.8678 (ttp) REVERT: E 215 ARG cc_start: 0.8873 (ttt90) cc_final: 0.8642 (ttt90) REVERT: E 243 MET cc_start: 0.8212 (mtp) cc_final: 0.7996 (mtm) REVERT: F 42 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7584 (mt-10) REVERT: F 58 LYS cc_start: 0.7385 (mtpt) cc_final: 0.6828 (mtpt) REVERT: F 210 MET cc_start: 0.8364 (mtp) cc_final: 0.7968 (mtp) outliers start: 24 outliers final: 9 residues processed: 249 average time/residue: 1.9124 time to fit residues: 509.9395 Evaluate side-chains 234 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN C 23 GLN C 202 GLN D 202 GLN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15768 Z= 0.296 Angle : 0.529 7.906 21488 Z= 0.282 Chirality : 0.041 0.134 2434 Planarity : 0.005 0.047 2632 Dihedral : 15.063 86.323 2702 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.91 (0.19), residues: 1878 helix: -0.36 (0.17), residues: 894 sheet: 0.31 (0.37), residues: 210 loop : -1.01 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 93 PHE 0.013 0.002 PHE A 92 TYR 0.014 0.002 TYR B 315 ARG 0.005 0.001 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 206 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: A 326 MET cc_start: 0.8205 (ttp) cc_final: 0.7882 (mtp) REVERT: B 27 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6348 (tpt90) REVERT: B 30 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.5430 (mp10) REVERT: B 57 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7647 (tttt) REVERT: B 73 LYS cc_start: 0.7976 (tttp) cc_final: 0.7669 (ttpt) REVERT: B 161 ASP cc_start: 0.8705 (t70) cc_final: 0.8445 (t70) REVERT: B 165 THR cc_start: 0.8427 (m) cc_final: 0.8138 (p) REVERT: B 326 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7761 (tmm) REVERT: C 176 GLU cc_start: 0.8024 (tp30) cc_final: 0.7580 (tp30) REVERT: C 205 TYR cc_start: 0.8444 (m-80) cc_final: 0.8084 (m-80) REVERT: C 306 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7033 (tmm160) REVERT: D 43 GLU cc_start: 0.7674 (mt-10) cc_final: 0.6943 (mp0) REVERT: D 73 LYS cc_start: 0.8511 (tttt) cc_final: 0.8268 (tttt) REVERT: D 111 LYS cc_start: 0.8220 (mttp) cc_final: 0.7780 (mtmt) REVERT: D 177 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: E 27 ARG cc_start: 0.7340 (ttm170) cc_final: 0.6839 (mtm-85) REVERT: E 39 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7683 (ptmt) REVERT: E 40 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7269 (mmtp) REVERT: E 111 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7567 (mttt) REVERT: E 158 MET cc_start: 0.8941 (ttm) cc_final: 0.8689 (ttp) REVERT: E 215 ARG cc_start: 0.8907 (ttt90) cc_final: 0.8661 (ttt90) REVERT: F 210 MET cc_start: 0.8379 (mtp) cc_final: 0.7990 (mtp) outliers start: 39 outliers final: 19 residues processed: 251 average time/residue: 1.8860 time to fit residues: 506.6246 Evaluate side-chains 256 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 0.0370 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15768 Z= 0.180 Angle : 0.469 6.351 21488 Z= 0.254 Chirality : 0.039 0.138 2434 Planarity : 0.004 0.045 2632 Dihedral : 15.012 88.233 2702 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.32 % Allowed : 25.83 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.74 (0.19), residues: 1878 helix: -0.15 (0.17), residues: 882 sheet: 0.33 (0.37), residues: 210 loop : -1.00 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 93 PHE 0.011 0.001 PHE F 46 TYR 0.011 0.001 TYR B 315 ARG 0.010 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 206 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: A 326 MET cc_start: 0.8236 (ttp) cc_final: 0.7932 (mtp) REVERT: B 27 ARG cc_start: 0.7528 (mtp180) cc_final: 0.6327 (tpt90) REVERT: B 30 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.5346 (mp10) REVERT: B 57 LYS cc_start: 0.7936 (mmmt) cc_final: 0.7454 (tttt) REVERT: B 161 ASP cc_start: 0.8636 (t70) cc_final: 0.8359 (t70) REVERT: B 165 THR cc_start: 0.8470 (m) cc_final: 0.8138 (p) REVERT: B 326 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7705 (tmm) REVERT: C 70 LYS cc_start: 0.6966 (mmtm) cc_final: 0.6746 (mmmm) REVERT: C 176 GLU cc_start: 0.7978 (tp30) cc_final: 0.7570 (tp30) REVERT: C 205 TYR cc_start: 0.8469 (m-80) cc_final: 0.8190 (m-80) REVERT: C 306 ARG cc_start: 0.7556 (tmm-80) cc_final: 0.6933 (tmm160) REVERT: C 308 GLU cc_start: 0.8336 (pm20) cc_final: 0.8133 (pm20) REVERT: D 43 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6875 (mp0) REVERT: D 73 LYS cc_start: 0.8571 (tttt) cc_final: 0.8334 (tttt) REVERT: D 111 LYS cc_start: 0.8221 (mttp) cc_final: 0.7772 (mtmt) REVERT: E 27 ARG cc_start: 0.7360 (ttm170) cc_final: 0.6947 (mtm-85) REVERT: E 39 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7764 (ptmt) REVERT: E 40 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7268 (mmtp) REVERT: E 111 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7566 (mttt) REVERT: E 158 MET cc_start: 0.8930 (ttm) cc_final: 0.8671 (ttp) REVERT: E 215 ARG cc_start: 0.8895 (ttt90) cc_final: 0.8670 (ttt90) REVERT: E 243 MET cc_start: 0.8234 (mtp) cc_final: 0.8013 (mtm) REVERT: F 58 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6904 (mtpt) REVERT: F 210 MET cc_start: 0.8506 (mtp) cc_final: 0.8124 (mtp) outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 1.9013 time to fit residues: 508.9538 Evaluate side-chains 248 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 229 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15768 Z= 0.151 Angle : 0.451 6.378 21488 Z= 0.245 Chirality : 0.038 0.137 2434 Planarity : 0.004 0.045 2632 Dihedral : 14.930 89.649 2702 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.79 % Allowed : 26.56 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.59 (0.19), residues: 1878 helix: -0.05 (0.18), residues: 888 sheet: 0.15 (0.33), residues: 264 loop : -0.87 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.010 0.001 PHE F 46 TYR 0.010 0.001 TYR E 54 ARG 0.010 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7572 (mm-30) REVERT: A 326 MET cc_start: 0.8234 (ttp) cc_final: 0.7915 (mtp) REVERT: B 27 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6326 (tpt90) REVERT: B 30 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5372 (mp10) REVERT: B 57 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7434 (tttt) REVERT: B 161 ASP cc_start: 0.8624 (t70) cc_final: 0.8337 (t70) REVERT: B 165 THR cc_start: 0.8446 (m) cc_final: 0.8116 (p) REVERT: B 251 MET cc_start: 0.8352 (mtp) cc_final: 0.8119 (mtp) REVERT: B 326 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: C 70 LYS cc_start: 0.6882 (mmtm) cc_final: 0.6644 (mmmm) REVERT: C 176 GLU cc_start: 0.7860 (tp30) cc_final: 0.7429 (tp30) REVERT: C 306 ARG cc_start: 0.7508 (tmm-80) cc_final: 0.6872 (tmm160) REVERT: D 43 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6810 (mp0) REVERT: D 73 LYS cc_start: 0.8559 (tttt) cc_final: 0.8312 (tttt) REVERT: D 111 LYS cc_start: 0.8219 (mttp) cc_final: 0.7770 (mtmt) REVERT: D 177 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8339 (ttt-90) REVERT: E 39 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7762 (ptmt) REVERT: E 111 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7550 (mttt) REVERT: E 158 MET cc_start: 0.8950 (ttm) cc_final: 0.8692 (ttp) REVERT: E 215 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8618 (ttt90) REVERT: E 243 MET cc_start: 0.8226 (mtp) cc_final: 0.7980 (mtm) REVERT: F 58 LYS cc_start: 0.7443 (mtpt) cc_final: 0.6889 (mtpt) REVERT: F 210 MET cc_start: 0.8398 (mtp) cc_final: 0.7980 (mtp) outliers start: 21 outliers final: 11 residues processed: 242 average time/residue: 1.8468 time to fit residues: 478.6708 Evaluate side-chains 243 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 0.0870 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 196 ASN A 206 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15768 Z= 0.157 Angle : 0.456 7.376 21488 Z= 0.246 Chirality : 0.038 0.139 2434 Planarity : 0.004 0.045 2632 Dihedral : 14.885 89.251 2702 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.99 % Allowed : 26.69 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.52 (0.19), residues: 1878 helix: 0.01 (0.18), residues: 888 sheet: 0.22 (0.33), residues: 264 loop : -0.85 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.011 0.001 PHE F 46 TYR 0.010 0.001 TYR B 315 ARG 0.009 0.000 ARG B 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 326 MET cc_start: 0.8208 (ttp) cc_final: 0.7908 (mtp) REVERT: B 27 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6365 (tpt90) REVERT: B 30 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.5427 (mp10) REVERT: B 57 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7367 (tttt) REVERT: B 161 ASP cc_start: 0.8624 (t70) cc_final: 0.8338 (t70) REVERT: B 165 THR cc_start: 0.8483 (m) cc_final: 0.8132 (p) REVERT: B 326 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7509 (tmm) REVERT: C 70 LYS cc_start: 0.6890 (mmtm) cc_final: 0.6648 (mmmm) REVERT: C 176 GLU cc_start: 0.7861 (tp30) cc_final: 0.7431 (tp30) REVERT: C 306 ARG cc_start: 0.7507 (tmm-80) cc_final: 0.6873 (tmm160) REVERT: D 43 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6826 (mp0) REVERT: D 73 LYS cc_start: 0.8442 (tttt) cc_final: 0.8192 (tttt) REVERT: D 111 LYS cc_start: 0.8220 (mttp) cc_final: 0.7774 (mtmt) REVERT: D 177 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8344 (ttt-90) REVERT: E 27 ARG cc_start: 0.7003 (mtm180) cc_final: 0.6619 (mtm-85) REVERT: E 39 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7771 (ptmt) REVERT: E 111 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7539 (mttt) REVERT: E 158 MET cc_start: 0.8941 (ttm) cc_final: 0.8688 (ttp) REVERT: E 215 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8619 (ttt90) REVERT: E 243 MET cc_start: 0.8232 (mtp) cc_final: 0.7979 (mtm) REVERT: F 58 LYS cc_start: 0.7377 (mtpt) cc_final: 0.6827 (mtpt) REVERT: F 210 MET cc_start: 0.8376 (mtp) cc_final: 0.7962 (mtp) outliers start: 24 outliers final: 14 residues processed: 244 average time/residue: 1.9063 time to fit residues: 497.0789 Evaluate side-chains 244 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 296 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 8 optimal weight: 0.0270 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097523 restraints weight = 62533.842| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.29 r_work: 0.2598 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15768 Z= 0.129 Angle : 0.437 6.317 21488 Z= 0.237 Chirality : 0.038 0.143 2434 Planarity : 0.004 0.045 2632 Dihedral : 14.805 89.188 2702 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.46 % Allowed : 27.49 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: -0.37 (0.20), residues: 1878 helix: 0.14 (0.18), residues: 882 sheet: 0.30 (0.33), residues: 264 loop : -0.78 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 199 PHE 0.009 0.001 PHE A 126 TYR 0.009 0.001 TYR E 54 ARG 0.009 0.000 ARG B 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.21 seconds wall clock time: 139 minutes 48.49 seconds (8388.49 seconds total)