Starting phenix.real_space_refine on Sat Mar 23 22:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu7_26128/03_2024/7tu7_26128_updated.pdb" } resolution = 2.5 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= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19218 atoms to isotropic. 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 P 18 5.49 5 Mg 18 5.21 5 S 48 5.16 5 C 12744 2.51 5 N 3426 2.21 5 O 3678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 367": "OE1" <-> "OE2" Residue "F TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 367": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19932 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "C" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "D" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "E" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3288 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.73, per 1000 atoms: 0.54 Number of scatterers: 19932 At special positions: 0 Unit cell: (129.548, 137.936, 97.86, 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) S 48 16.00 P 18 15.00 Mg 18 11.99 O 3678 8.00 N 3426 7.00 C 12744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 3.8 seconds 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 63.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 7 No H-bonds generated for 'chain 'A' and resid 4 through 7' Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.779A pdb=" N ASP A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.856A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 90 Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.771A pdb=" N GLN A 96 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.912A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.725A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 4.400A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 244 through 268 removed outlier: 4.045A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.938A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 299 through 324 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 363 through 388 removed outlier: 3.608A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'B' and resid 4 through 7 No H-bonds generated for 'chain 'B' and resid 4 through 7' Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.778A pdb=" N ASP B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.856A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.772A pdb=" N GLN B 96 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.912A pdb=" N GLY B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.725A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.400A pdb=" N ASP B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 244 through 268 removed outlier: 4.045A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.938A pdb=" N LEU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 299 through 324 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 363 through 388 removed outlier: 3.608A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 412 through 424 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.778A pdb=" N ASP C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.856A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 90 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.772A pdb=" N GLN C 96 " --> pdb=" O HIS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.913A pdb=" N GLY C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.725A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.400A pdb=" N ASP C 145 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 244 through 268 removed outlier: 4.046A pdb=" N LEU C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.937A pdb=" N LEU C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 299 through 324 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 363 through 388 removed outlier: 3.607A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 439 Processing helix chain 'D' and resid 4 through 7 No H-bonds generated for 'chain 'D' and resid 4 through 7' Processing helix chain 'D' and resid 30 through 39 removed outlier: 3.779A pdb=" N ASP D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.856A pdb=" N LEU D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 90 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.772A pdb=" N GLN D 96 " --> pdb=" O HIS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 removed outlier: 3.912A pdb=" N GLY D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.724A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 4.399A pdb=" N ASP D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 156 Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'D' and resid 244 through 268 removed outlier: 4.045A pdb=" N LEU D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 3.938A pdb=" N LEU D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 299 through 324 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 363 through 388 removed outlier: 3.608A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 412 through 424 Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 30 through 39 removed outlier: 3.778A pdb=" N ASP E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.856A pdb=" N LEU E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP E 49 " --> pdb=" O ARG E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 90 Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.771A pdb=" N GLN E 96 " --> pdb=" O HIS E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.912A pdb=" N GLY E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.725A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 4.400A pdb=" N ASP E 145 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 156 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 183 through 189 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 244 through 268 removed outlier: 4.045A pdb=" N LEU E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 removed outlier: 3.938A pdb=" N LEU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 284 No H-bonds generated for 'chain 'E' and resid 281 through 284' Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 299 through 324 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 345 through 358 Processing helix chain 'E' and resid 363 through 388 removed outlier: 3.608A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 402 Processing helix chain 'E' and resid 412 through 424 Processing helix chain 'E' and resid 428 through 439 Processing helix chain 'F' and resid 4 through 7 No H-bonds generated for 'chain 'F' and resid 4 through 7' Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.778A pdb=" N ASP F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.857A pdb=" N LEU F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN F 48 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 90 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.771A pdb=" N GLN F 96 " --> pdb=" O HIS F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.912A pdb=" N GLY F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.725A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 4.400A pdb=" N ASP F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 183 through 189 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 244 through 268 removed outlier: 4.045A pdb=" N LEU F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 removed outlier: 3.939A pdb=" N LEU F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 284 No H-bonds generated for 'chain 'F' and resid 281 through 284' Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 299 through 324 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 345 through 358 Processing helix chain 'F' and resid 363 through 388 removed outlier: 3.608A pdb=" N GLU F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 412 through 424 Processing helix chain 'F' and resid 428 through 439 1002 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 8.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3210 1.30 - 1.42: 5328 1.42 - 1.55: 11652 1.55 - 1.68: 36 1.68 - 1.80: 78 Bond restraints: 20304 Sorted by residual: bond pdb=" C2' DGT E 501 " pdb=" C3' DGT E 501 " ideal model delta sigma weight residual 1.284 1.521 -0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C2' DGT C 501 " pdb=" C3' DGT C 501 " ideal model delta sigma weight residual 1.284 1.521 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' DGT D 501 " pdb=" C3' DGT D 501 " ideal model delta sigma weight residual 1.284 1.521 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' DGT F 501 " pdb=" C3' DGT F 501 " ideal model delta sigma weight residual 1.284 1.521 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C2' DGT A 501 " pdb=" C3' DGT A 501 " ideal model delta sigma weight residual 1.284 1.520 -0.236 2.00e-02 2.50e+03 1.40e+02 ... (remaining 20299 not shown) Histogram of bond angle deviations from ideal: 99.27 - 107.42: 526 107.42 - 115.58: 12291 115.58 - 123.73: 14304 123.73 - 131.88: 389 131.88 - 140.04: 24 Bond angle restraints: 27534 Sorted by residual: angle pdb=" PB DGT F 501 " pdb=" O3B DGT F 501 " pdb=" PG DGT F 501 " ideal model delta sigma weight residual 123.56 140.04 -16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" PB DGT B 501 " pdb=" O3B DGT B 501 " pdb=" PG DGT B 501 " ideal model delta sigma weight residual 123.56 140.01 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" PB DGT D 501 " pdb=" O3B DGT D 501 " pdb=" PG DGT D 501 " ideal model delta sigma weight residual 123.56 140.01 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" PB DGT C 501 " pdb=" O3B DGT C 501 " pdb=" PG DGT C 501 " ideal model delta sigma weight residual 123.56 140.01 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" PB DGT A 501 " pdb=" O3B DGT A 501 " pdb=" PG DGT A 501 " ideal model delta sigma weight residual 123.56 140.00 -16.44 3.00e+00 1.11e-01 3.00e+01 ... (remaining 27529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.29: 10644 20.29 - 40.58: 1098 40.58 - 60.87: 246 60.87 - 81.15: 48 81.15 - 101.44: 12 Dihedral angle restraints: 12048 sinusoidal: 4518 harmonic: 7530 Sorted by residual: dihedral pdb=" O1B DGT C 501 " pdb=" O3B DGT C 501 " pdb=" PB DGT C 501 " pdb=" PG DGT C 501 " ideal model delta sinusoidal sigma weight residual -58.32 -159.76 101.44 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" O1B DGT F 501 " pdb=" O3B DGT F 501 " pdb=" PB DGT F 501 " pdb=" PG DGT F 501 " ideal model delta sinusoidal sigma weight residual -58.32 -159.73 101.41 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" O1B DGT A 501 " pdb=" O3B DGT A 501 " pdb=" PB DGT A 501 " pdb=" PG DGT A 501 " ideal model delta sinusoidal sigma weight residual -58.32 -159.73 101.41 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2551 0.051 - 0.102: 514 0.102 - 0.152: 55 0.152 - 0.203: 6 0.203 - 0.254: 6 Chirality restraints: 3132 Sorted by residual: chirality pdb=" C3' DGT D 501 " pdb=" C2' DGT D 501 " pdb=" C4' DGT D 501 " pdb=" O3' DGT D 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.68 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' DGT C 501 " pdb=" C2' DGT C 501 " pdb=" C4' DGT C 501 " pdb=" O3' DGT C 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.68 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' DGT F 501 " pdb=" C2' DGT F 501 " pdb=" C4' DGT F 501 " pdb=" O3' DGT F 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.68 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3129 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 117 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" CG ASP A 117 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 117 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 117 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 117 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" CG ASP D 117 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP D 117 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP D 117 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 117 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" CG ASP B 117 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP B 117 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 117 " 0.018 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 102 2.54 - 3.13: 14793 3.13 - 3.72: 30145 3.72 - 4.31: 42260 4.31 - 4.90: 72238 Nonbonded interactions: 159538 Sorted by model distance: nonbonded pdb=" NE2 HIS E 68 " pdb="MG MG E 502 " model vdw 1.947 2.250 nonbonded pdb=" NE2 HIS C 68 " pdb="MG MG C 502 " model vdw 1.948 2.250 nonbonded pdb=" NE2 HIS B 68 " pdb="MG MG B 502 " model vdw 1.948 2.250 nonbonded pdb=" NE2 HIS D 68 " pdb="MG MG D 502 " model vdw 1.948 2.250 nonbonded pdb=" NE2 HIS A 68 " pdb="MG MG A 502 " model vdw 1.948 2.250 ... (remaining 159533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.020 Extract box with map and model: 3.750 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 54.270 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.010 0.237 20304 Z= 0.639 Angle : 0.777 16.476 27534 Z= 0.384 Chirality : 0.042 0.254 3132 Planarity : 0.005 0.049 3468 Dihedral : 17.474 101.444 7224 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.92 % Allowed : 22.02 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2550 helix: 1.34 (0.13), residues: 1626 sheet: None (None), residues: 0 loop : -1.16 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 240 HIS 0.007 0.001 HIS F 243 PHE 0.010 0.002 PHE C 262 TYR 0.017 0.002 TYR C 257 ARG 0.008 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 543 time to evaluate : 2.299 Fit side-chains REVERT: B 34 ASP cc_start: 0.7709 (m-30) cc_final: 0.7485 (m-30) REVERT: B 49 ASP cc_start: 0.6950 (t0) cc_final: 0.6618 (t70) REVERT: B 81 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7933 (mtt90) REVERT: B 91 TYR cc_start: 0.8178 (m-80) cc_final: 0.7919 (m-80) REVERT: B 101 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7946 (mttp) REVERT: B 232 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7672 (mtp85) REVERT: C 49 ASP cc_start: 0.6870 (t0) cc_final: 0.6557 (t70) REVERT: C 101 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7561 (mttp) REVERT: C 104 ASP cc_start: 0.7592 (m-30) cc_final: 0.7392 (m-30) REVERT: C 268 LEU cc_start: 0.8437 (mt) cc_final: 0.8201 (mt) REVERT: C 280 MET cc_start: 0.8154 (mtp) cc_final: 0.7890 (mtp) REVERT: C 294 ASN cc_start: 0.8049 (m-40) cc_final: 0.7821 (m110) REVERT: C 347 GLN cc_start: 0.8161 (mp10) cc_final: 0.7929 (mp-120) REVERT: C 415 ASN cc_start: 0.8331 (m110) cc_final: 0.8075 (m-40) REVERT: D 101 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7693 (mttp) REVERT: D 142 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7693 (ptm160) REVERT: D 280 MET cc_start: 0.8265 (mtp) cc_final: 0.8028 (mtp) REVERT: E 195 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7048 (mt-10) REVERT: E 217 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7621 (ttt180) REVERT: E 287 THR cc_start: 0.8212 (m) cc_final: 0.7957 (p) REVERT: E 367 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6410 (mt-10) REVERT: F 139 TYR cc_start: 0.8062 (t80) cc_final: 0.7496 (t80) REVERT: F 287 THR cc_start: 0.8386 (m) cc_final: 0.8135 (p) REVERT: F 367 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6561 (mt-10) outliers start: 18 outliers final: 8 residues processed: 552 average time/residue: 1.4888 time to fit residues: 910.6592 Evaluate side-chains 538 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 530 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN B 137 ASN C 52 GLN C 137 ASN C 153 GLN D 52 GLN D 137 ASN E 153 GLN F 52 GLN F 137 ASN F 153 GLN F 347 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20304 Z= 0.231 Angle : 0.474 6.035 27534 Z= 0.259 Chirality : 0.037 0.144 3132 Planarity : 0.004 0.044 3468 Dihedral : 7.668 95.762 2890 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.55 % Allowed : 20.69 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2550 helix: 1.81 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.14 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 240 HIS 0.007 0.001 HIS B 116 PHE 0.015 0.002 PHE F 220 TYR 0.022 0.002 TYR C 257 ARG 0.006 0.000 ARG F 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 519 time to evaluate : 2.541 Fit side-chains REVERT: B 32 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6491 (mm-30) REVERT: B 49 ASP cc_start: 0.6944 (t0) cc_final: 0.6683 (t70) REVERT: B 81 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7997 (mtt90) REVERT: B 441 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7852 (mt) REVERT: C 49 ASP cc_start: 0.6910 (t0) cc_final: 0.6578 (t70) REVERT: C 101 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7725 (mmtp) REVERT: C 104 ASP cc_start: 0.7582 (m-30) cc_final: 0.7319 (m-30) REVERT: C 280 MET cc_start: 0.8220 (mtp) cc_final: 0.7881 (mtt) REVERT: E 191 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7885 (ptpt) REVERT: E 287 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7994 (p) REVERT: F 287 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8154 (p) outliers start: 50 outliers final: 15 residues processed: 538 average time/residue: 1.5163 time to fit residues: 902.6517 Evaluate side-chains 529 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 510 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 417 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 137 ASN B 52 GLN B 137 ASN B 170 GLN B 347 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 137 ASN C 170 GLN D 52 GLN E 153 GLN F 137 ASN F 153 GLN F 170 GLN F 347 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 20304 Z= 0.519 Angle : 0.625 6.534 27534 Z= 0.338 Chirality : 0.046 0.189 3132 Planarity : 0.005 0.050 3468 Dihedral : 7.861 106.572 2881 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.67 % Allowed : 19.06 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2550 helix: 1.41 (0.12), residues: 1614 sheet: None (None), residues: 0 loop : -1.17 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 240 HIS 0.010 0.002 HIS C 116 PHE 0.027 0.003 PHE F 220 TYR 0.021 0.002 TYR E 257 ARG 0.006 0.001 ARG F 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 514 time to evaluate : 2.195 Fit side-chains REVERT: B 32 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6616 (mm-30) REVERT: B 49 ASP cc_start: 0.7023 (t0) cc_final: 0.6678 (t70) REVERT: B 81 ARG cc_start: 0.8325 (mtt90) cc_final: 0.8086 (mtt90) REVERT: C 49 ASP cc_start: 0.6945 (t0) cc_final: 0.6623 (t70) REVERT: C 104 ASP cc_start: 0.7575 (m-30) cc_final: 0.7308 (m-30) REVERT: C 280 MET cc_start: 0.8227 (mtp) cc_final: 0.7910 (mtt) REVERT: C 441 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7838 (mt) REVERT: D 101 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7791 (mmtp) REVERT: D 153 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: E 101 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7974 (mmtp) REVERT: E 287 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7994 (p) REVERT: E 374 GLU cc_start: 0.6679 (tp30) cc_final: 0.6470 (tp30) REVERT: F 287 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8092 (p) outliers start: 72 outliers final: 33 residues processed: 542 average time/residue: 1.5041 time to fit residues: 903.9190 Evaluate side-chains 555 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 516 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 347 GLN D 137 ASN E 153 GLN F 137 ASN F 153 GLN ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20304 Z= 0.172 Angle : 0.438 5.618 27534 Z= 0.241 Chirality : 0.035 0.131 3132 Planarity : 0.004 0.043 3468 Dihedral : 7.094 96.264 2881 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.14 % Allowed : 21.15 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2550 helix: 2.02 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.00 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.003 0.001 HIS B 116 PHE 0.014 0.001 PHE F 220 TYR 0.022 0.001 TYR D 257 ARG 0.006 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 511 time to evaluate : 2.454 Fit side-chains REVERT: B 32 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6482 (mm-30) REVERT: B 49 ASP cc_start: 0.6988 (t0) cc_final: 0.6667 (t70) REVERT: B 81 ARG cc_start: 0.8249 (mtt90) cc_final: 0.8017 (mtt90) REVERT: C 49 ASP cc_start: 0.6926 (t0) cc_final: 0.6609 (t70) REVERT: C 104 ASP cc_start: 0.7591 (m-30) cc_final: 0.7334 (m-30) REVERT: C 280 MET cc_start: 0.8201 (mtp) cc_final: 0.7872 (mtt) REVERT: C 441 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7766 (mt) REVERT: D 253 ASP cc_start: 0.8139 (t0) cc_final: 0.7931 (t70) REVERT: E 94 LEU cc_start: 0.8597 (mt) cc_final: 0.8340 (mt) REVERT: E 287 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7953 (p) REVERT: F 287 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8027 (p) REVERT: F 374 GLU cc_start: 0.6596 (tp30) cc_final: 0.6374 (tp30) outliers start: 42 outliers final: 18 residues processed: 531 average time/residue: 1.4725 time to fit residues: 869.3261 Evaluate side-chains 520 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 499 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 185 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 223 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 347 GLN C 347 GLN D 137 ASN D 161 ASN E 137 ASN E 153 GLN F 137 ASN F 153 GLN F 343 ASN F 347 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20304 Z= 0.211 Angle : 0.460 5.939 27534 Z= 0.252 Chirality : 0.036 0.143 3132 Planarity : 0.004 0.043 3468 Dihedral : 6.886 93.365 2880 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.50 % Allowed : 21.61 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2550 helix: 1.95 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.07 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.005 0.001 HIS B 116 PHE 0.016 0.002 PHE F 220 TYR 0.023 0.001 TYR C 257 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 502 time to evaluate : 2.441 Fit side-chains REVERT: B 32 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6510 (mm-30) REVERT: B 49 ASP cc_start: 0.6999 (t0) cc_final: 0.6788 (t70) REVERT: B 81 ARG cc_start: 0.8249 (mtt90) cc_final: 0.8021 (mtt90) REVERT: C 49 ASP cc_start: 0.6928 (t0) cc_final: 0.6621 (t70) REVERT: C 104 ASP cc_start: 0.7588 (m-30) cc_final: 0.7323 (m-30) REVERT: C 280 MET cc_start: 0.8181 (mtp) cc_final: 0.7815 (mtt) REVERT: D 153 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: E 94 LEU cc_start: 0.8608 (mt) cc_final: 0.8388 (mt) REVERT: E 101 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7894 (mmtp) REVERT: E 253 ASP cc_start: 0.8259 (t0) cc_final: 0.8058 (t0) REVERT: E 287 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7950 (p) REVERT: E 367 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6358 (mp0) REVERT: F 287 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8033 (p) REVERT: F 374 GLU cc_start: 0.6640 (tp30) cc_final: 0.6393 (tp30) outliers start: 49 outliers final: 24 residues processed: 522 average time/residue: 1.4975 time to fit residues: 867.5902 Evaluate side-chains 522 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 494 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.0170 chunk 131 optimal weight: 0.0050 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 347 GLN C 199 HIS C 347 GLN D 137 ASN E 137 ASN E 153 GLN F 137 ASN F 153 GLN F 347 GLN ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20304 Z= 0.115 Angle : 0.391 5.064 27534 Z= 0.213 Chirality : 0.033 0.127 3132 Planarity : 0.003 0.040 3468 Dihedral : 6.056 73.967 2880 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.19 % Allowed : 22.27 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2550 helix: 2.14 (0.13), residues: 1650 sheet: None (None), residues: 0 loop : -0.85 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.003 0.000 HIS F 116 PHE 0.012 0.001 PHE A 102 TYR 0.022 0.001 TYR B 257 ARG 0.007 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 497 time to evaluate : 2.622 Fit side-chains REVERT: A 323 MET cc_start: 0.7239 (tpt) cc_final: 0.6998 (mmp) REVERT: B 32 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6479 (mm-30) REVERT: B 49 ASP cc_start: 0.6972 (t0) cc_final: 0.6702 (t70) REVERT: B 81 ARG cc_start: 0.8201 (mtt90) cc_final: 0.8000 (mtt90) REVERT: B 253 ASP cc_start: 0.8074 (t0) cc_final: 0.7831 (t70) REVERT: C 49 ASP cc_start: 0.6863 (t0) cc_final: 0.6577 (t70) REVERT: C 104 ASP cc_start: 0.7607 (m-30) cc_final: 0.7347 (m-30) REVERT: C 280 MET cc_start: 0.8120 (mtp) cc_final: 0.7842 (mtt) REVERT: D 159 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: D 323 MET cc_start: 0.7292 (tpt) cc_final: 0.7030 (mmm) REVERT: E 94 LEU cc_start: 0.8602 (mt) cc_final: 0.8374 (mt) REVERT: E 101 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7821 (mmtp) REVERT: E 287 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7949 (p) REVERT: F 287 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.8033 (p) REVERT: F 317 GLU cc_start: 0.7259 (tt0) cc_final: 0.7029 (tt0) REVERT: F 401 LEU cc_start: 0.8269 (tp) cc_final: 0.8057 (tt) outliers start: 43 outliers final: 19 residues processed: 518 average time/residue: 1.4961 time to fit residues: 860.2125 Evaluate side-chains 509 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 486 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 343 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 347 GLN D 137 ASN E 137 ASN E 153 GLN E 170 GLN F 137 ASN F 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 20304 Z= 0.466 Angle : 0.596 6.478 27534 Z= 0.322 Chirality : 0.045 0.185 3132 Planarity : 0.004 0.045 3468 Dihedral : 6.900 89.160 2880 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.55 % Allowed : 21.61 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2550 helix: 1.63 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 240 HIS 0.009 0.002 HIS A 243 PHE 0.025 0.003 PHE F 220 TYR 0.029 0.002 TYR F 257 ARG 0.007 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 509 time to evaluate : 2.187 Fit side-chains REVERT: B 32 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6588 (mm-30) REVERT: B 34 ASP cc_start: 0.7732 (m-30) cc_final: 0.7482 (m-30) REVERT: B 49 ASP cc_start: 0.7032 (t0) cc_final: 0.6821 (t70) REVERT: B 81 ARG cc_start: 0.8272 (mtt90) cc_final: 0.8059 (mtt90) REVERT: C 104 ASP cc_start: 0.7587 (m-30) cc_final: 0.7322 (m-30) REVERT: C 280 MET cc_start: 0.8186 (mtp) cc_final: 0.7913 (mtt) REVERT: D 153 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: D 385 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7559 (mtt-85) REVERT: E 101 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7896 (mmtp) REVERT: E 287 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.8009 (p) REVERT: F 287 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8085 (p) REVERT: F 374 GLU cc_start: 0.6620 (tp30) cc_final: 0.6358 (tp30) outliers start: 50 outliers final: 26 residues processed: 529 average time/residue: 1.4719 time to fit residues: 864.4813 Evaluate side-chains 533 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 503 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN B 347 GLN C 347 GLN D 137 ASN E 137 ASN E 153 GLN E 170 GLN F 48 GLN F 137 ASN F 153 GLN F 170 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20304 Z= 0.199 Angle : 0.463 5.749 27534 Z= 0.254 Chirality : 0.036 0.138 3132 Planarity : 0.004 0.042 3468 Dihedral : 6.507 82.977 2880 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.63 % Allowed : 22.78 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2550 helix: 1.89 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.005 0.001 HIS B 116 PHE 0.013 0.001 PHE E 220 TYR 0.023 0.001 TYR B 257 ARG 0.007 0.000 ARG F 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 489 time to evaluate : 2.324 Fit side-chains REVERT: B 32 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6513 (mm-30) REVERT: B 34 ASP cc_start: 0.7662 (m-30) cc_final: 0.7428 (m-30) REVERT: B 49 ASP cc_start: 0.7013 (t0) cc_final: 0.6803 (t70) REVERT: B 81 ARG cc_start: 0.8241 (mtt90) cc_final: 0.8024 (mtt90) REVERT: C 104 ASP cc_start: 0.7586 (m-30) cc_final: 0.7322 (m-30) REVERT: C 280 MET cc_start: 0.8163 (mtp) cc_final: 0.7811 (mtt) REVERT: E 94 LEU cc_start: 0.8557 (mt) cc_final: 0.8315 (mt) REVERT: E 101 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (mmtp) REVERT: E 260 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7637 (mp) REVERT: E 287 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (p) REVERT: F 287 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (p) REVERT: F 369 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7138 (mt-10) outliers start: 32 outliers final: 20 residues processed: 504 average time/residue: 1.4825 time to fit residues: 829.1501 Evaluate side-chains 519 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 495 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN B 347 GLN C 347 GLN D 137 ASN E 137 ASN E 153 GLN E 170 GLN F 137 ASN F 153 GLN F 170 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20304 Z= 0.266 Angle : 0.500 6.179 27534 Z= 0.272 Chirality : 0.038 0.154 3132 Planarity : 0.004 0.043 3468 Dihedral : 6.526 83.248 2880 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 22.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2550 helix: 1.82 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.07 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 240 HIS 0.006 0.001 HIS B 116 PHE 0.017 0.002 PHE F 220 TYR 0.026 0.002 TYR E 257 ARG 0.007 0.000 ARG F 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 501 time to evaluate : 2.501 Fit side-chains REVERT: B 32 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6573 (mm-30) REVERT: B 34 ASP cc_start: 0.7686 (m-30) cc_final: 0.7454 (m-30) REVERT: B 49 ASP cc_start: 0.7022 (t0) cc_final: 0.6811 (t70) REVERT: B 260 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.7854 (mp) REVERT: B 317 GLU cc_start: 0.7151 (tt0) cc_final: 0.6944 (tt0) REVERT: C 104 ASP cc_start: 0.7579 (m-30) cc_final: 0.7312 (m-30) REVERT: C 280 MET cc_start: 0.8153 (mtp) cc_final: 0.7811 (mtt) REVERT: D 385 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7453 (mtt-85) REVERT: E 94 LEU cc_start: 0.8556 (mt) cc_final: 0.8323 (mt) REVERT: E 101 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7882 (mmtp) REVERT: E 260 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7643 (mp) REVERT: E 287 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7978 (p) REVERT: F 101 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7914 (mmtp) REVERT: F 287 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8059 (p) REVERT: F 374 GLU cc_start: 0.6655 (tp30) cc_final: 0.6414 (tp30) outliers start: 34 outliers final: 23 residues processed: 517 average time/residue: 1.4896 time to fit residues: 854.8438 Evaluate side-chains 533 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 504 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN B 347 GLN C 347 GLN D 137 ASN E 137 ASN E 153 GLN E 170 GLN F 137 ASN F 153 GLN F 170 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20304 Z= 0.347 Angle : 0.543 6.703 27534 Z= 0.296 Chirality : 0.040 0.169 3132 Planarity : 0.004 0.043 3468 Dihedral : 6.674 86.230 2880 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.78 % Allowed : 22.38 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2550 helix: 1.62 (0.13), residues: 1614 sheet: None (None), residues: 0 loop : -1.07 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 240 HIS 0.007 0.002 HIS B 116 PHE 0.022 0.002 PHE F 220 TYR 0.027 0.002 TYR E 257 ARG 0.007 0.001 ARG F 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 501 time to evaluate : 2.367 Fit side-chains REVERT: B 32 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6580 (mm-30) REVERT: B 34 ASP cc_start: 0.7722 (m-30) cc_final: 0.7486 (m-30) REVERT: B 49 ASP cc_start: 0.7034 (t0) cc_final: 0.6827 (t70) REVERT: B 260 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7815 (mp) REVERT: B 317 GLU cc_start: 0.7144 (tt0) cc_final: 0.6943 (tt0) REVERT: C 104 ASP cc_start: 0.7579 (m-30) cc_final: 0.7316 (m-30) REVERT: C 280 MET cc_start: 0.8150 (mtp) cc_final: 0.7854 (mtt) REVERT: D 159 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: D 385 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7507 (mtt-85) REVERT: E 94 LEU cc_start: 0.8550 (mt) cc_final: 0.8291 (mt) REVERT: E 101 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: E 260 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7664 (mp) REVERT: E 287 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7987 (p) REVERT: F 101 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7940 (mmtp) REVERT: F 287 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8062 (p) REVERT: F 374 GLU cc_start: 0.6678 (tp30) cc_final: 0.6418 (tp30) outliers start: 35 outliers final: 24 residues processed: 516 average time/residue: 1.4820 time to fit residues: 848.6039 Evaluate side-chains 531 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 500 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN B 347 GLN C 347 GLN D 6 HIS D 137 ASN E 137 ASN E 153 GLN E 170 GLN F 48 GLN F 137 ASN F 153 GLN F 170 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106741 restraints weight = 24559.822| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.40 r_work: 0.3232 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20304 Z= 0.183 Angle : 0.454 6.901 27534 Z= 0.250 Chirality : 0.035 0.138 3132 Planarity : 0.004 0.042 3468 Dihedral : 6.275 78.435 2880 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.78 % Allowed : 22.32 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2550 helix: 1.91 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -1.06 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.005 0.001 HIS D 116 PHE 0.013 0.001 PHE E 220 TYR 0.023 0.001 TYR C 257 ARG 0.007 0.000 ARG F 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11411.96 seconds wall clock time: 200 minutes 54.05 seconds (12054.05 seconds total)