Starting phenix.real_space_refine on Sun Mar 24 02:32:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/03_2024/7tu8_26129_updated.pdb" } resolution = 2.6 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= 0.047 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 19500 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 36 5.49 5 Mg 12 5.21 5 S 42 5.16 5 C 12858 2.51 5 N 3486 2.21 5 O 3798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ASP 428": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E ASP 388": "OD1" <-> "OD2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F ASP 428": "OD1" <-> "OD2" 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: 20232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "C" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "D" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "E" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "F" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3309 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 15, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' MG': 3, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' MG': 3, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' MG': 3, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' MG': 1, 'DGT': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.10, per 1000 atoms: 0.55 Number of scatterers: 20232 At special positions: 0 Unit cell: (129.548, 137.004, 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 42 16.00 P 36 15.00 Mg 12 11.99 O 3798 8.00 N 3486 7.00 C 12858 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: 6.65 Conformation dependent library (CDL) restraints added in 3.9 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 0 sheets defined 64.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 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 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.783A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.671A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.666A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'A' and resid 244 through 268 removed outlier: 4.239A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 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 removed outlier: 3.528A pdb=" N GLY A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) 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 389 removed outlier: 3.576A pdb=" N ASN A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 412 through 425 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 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.783A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.670A pdb=" N GLY B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.666A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'B' and resid 244 through 268 removed outlier: 4.238A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 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 removed outlier: 3.527A pdb=" N GLY B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) 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 389 removed outlier: 3.576A pdb=" N ASN B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 412 through 425 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 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.783A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.670A pdb=" N GLY C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.667A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'C' and resid 244 through 268 removed outlier: 4.238A pdb=" N LEU C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 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 removed outlier: 3.527A pdb=" N GLY C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) 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 389 removed outlier: 3.576A pdb=" N ASN C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 412 through 425 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 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.783A pdb=" N LEU D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'D' and resid 102 through 114 removed outlier: 3.670A pdb=" N GLY D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.666A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'D' and resid 244 through 268 removed outlier: 4.240A pdb=" N LEU D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 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 removed outlier: 3.528A pdb=" N GLY D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) 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 389 removed outlier: 3.577A pdb=" N ASN D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 412 through 425 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 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.783A pdb=" N LEU E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.670A pdb=" N GLY E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.666A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'E' and resid 244 through 268 removed outlier: 4.239A pdb=" N LEU E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 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 removed outlier: 3.528A pdb=" N GLY E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN E 316 " --> pdb=" O GLY E 312 " (cutoff:3.500A) 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 389 removed outlier: 3.576A pdb=" N ASN E 389 " --> pdb=" O ARG E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 402 Processing helix chain 'E' and resid 412 through 425 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 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 30 through 39 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.784A pdb=" N LEU F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN F 48 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 5.070A 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 97 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.670A pdb=" N GLY F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.666A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 4.520A 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 188 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 227 Processing helix chain 'F' and resid 244 through 268 removed outlier: 4.238A pdb=" N LEU F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 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 removed outlier: 3.528A pdb=" N GLY F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) 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 389 removed outlier: 3.577A pdb=" N ASN F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 412 through 425 Processing helix chain 'F' and resid 428 through 439 1026 hydrogen bonds defined for protein. 3006 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: 5.76 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3240 1.29 - 1.42: 5425 1.42 - 1.55: 11849 1.55 - 1.67: 42 1.67 - 1.80: 66 Bond restraints: 20622 Sorted by residual: bond pdb=" C2' DGT F 501 " pdb=" C3' DGT F 501 " ideal model delta sigma weight residual 1.284 1.522 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2' DGT B 501 " pdb=" C3' DGT B 501 " ideal model delta sigma weight residual 1.284 1.522 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2' DGT A 501 " pdb=" C3' DGT A 501 " ideal model delta sigma weight residual 1.284 1.522 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2' DGT C 501 " pdb=" C3' DGT C 501 " ideal model delta sigma weight residual 1.284 1.522 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2' DGT D 501 " pdb=" C3' DGT D 501 " ideal model delta sigma weight residual 1.284 1.522 -0.238 2.00e-02 2.50e+03 1.42e+02 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 99.67 - 107.78: 645 107.78 - 115.89: 12585 115.89 - 124.01: 14328 124.01 - 132.12: 402 132.12 - 140.23: 48 Bond angle restraints: 28008 Sorted by residual: angle pdb=" N ASN B 389 " pdb=" CA ASN B 389 " pdb=" C ASN B 389 " ideal model delta sigma weight residual 111.07 120.91 -9.84 1.07e+00 8.73e-01 8.45e+01 angle pdb=" N ASN D 389 " pdb=" CA ASN D 389 " pdb=" C ASN D 389 " ideal model delta sigma weight residual 111.07 120.91 -9.84 1.07e+00 8.73e-01 8.45e+01 angle pdb=" N ASN A 389 " pdb=" CA ASN A 389 " pdb=" C ASN A 389 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" N ASN C 389 " pdb=" CA ASN C 389 " pdb=" C ASN C 389 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.40e+01 angle pdb=" N ASN E 389 " pdb=" CA ASN E 389 " pdb=" C ASN E 389 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.40e+01 ... (remaining 28003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 11669 23.57 - 47.15: 505 47.15 - 70.72: 93 70.72 - 94.30: 33 94.30 - 117.87: 6 Dihedral angle restraints: 12306 sinusoidal: 4722 harmonic: 7584 Sorted by residual: dihedral pdb=" O1A DGT D 501 " pdb=" O3A DGT D 501 " pdb=" PA DGT D 501 " pdb=" PB DGT D 501 " ideal model delta sinusoidal sigma weight residual -80.64 37.23 -117.87 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" O1A DGT A 501 " pdb=" O3A DGT A 501 " pdb=" PA DGT A 501 " pdb=" PB DGT A 501 " ideal model delta sinusoidal sigma weight residual -80.64 37.19 -117.83 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" O1A DGT C 501 " pdb=" O3A DGT C 501 " pdb=" PA DGT C 501 " pdb=" PB DGT C 501 " ideal model delta sinusoidal sigma weight residual -80.64 37.19 -117.83 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 12303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2847 0.068 - 0.136: 267 0.136 - 0.205: 18 0.205 - 0.273: 12 0.273 - 0.341: 18 Chirality restraints: 3162 Sorted by residual: chirality pdb=" CA ASN E 389 " pdb=" N ASN E 389 " pdb=" C ASN E 389 " pdb=" CB ASN E 389 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ASN F 389 " pdb=" N ASN F 389 " pdb=" C ASN F 389 " pdb=" CB ASN F 389 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA ASN D 389 " pdb=" N ASN D 389 " pdb=" C ASN D 389 " pdb=" CB ASN D 389 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 3159 not shown) Planarity restraints: 3510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 116 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C HIS C 116 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS C 116 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP C 117 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 116 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C HIS F 116 " 0.030 2.00e-02 2.50e+03 pdb=" O HIS F 116 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP F 117 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 116 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C HIS D 116 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS D 116 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP D 117 " 0.011 2.00e-02 2.50e+03 ... (remaining 3507 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 42 2.48 - 3.08: 13759 3.08 - 3.69: 29520 3.69 - 4.29: 43971 4.29 - 4.90: 75401 Nonbonded interactions: 162693 Sorted by model distance: nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 503 " model vdw 1.874 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 503 " model vdw 1.875 2.250 nonbonded pdb=" NE2 HIS F 116 " pdb="MG MG F 503 " model vdw 1.875 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 503 " model vdw 1.875 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 503 " model vdw 1.875 2.250 ... (remaining 162688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 441 or resid 501 through 503)) selection = chain 'B' selection = (chain 'C' and (resid 3 through 441 or resid 501 through 503)) selection = chain 'D' selection = (chain 'E' and (resid 3 through 441 or resid 501 through 503)) 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 3.820 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 53.330 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.011 0.238 20622 Z= 0.696 Angle : 0.809 16.667 28008 Z= 0.448 Chirality : 0.050 0.341 3162 Planarity : 0.004 0.039 3510 Dihedral : 14.506 117.871 7446 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.45 (0.16), residues: 2568 helix: 1.04 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.08 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 240 HIS 0.005 0.002 HIS B 68 PHE 0.012 0.002 PHE F 334 TYR 0.024 0.002 TYR C 257 ARG 0.002 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 2.559 Fit side-chains REVERT: A 22 ILE cc_start: 0.8148 (pt) cc_final: 0.7897 (OUTLIER) REVERT: A 253 ASP cc_start: 0.7892 (t70) cc_final: 0.7657 (t0) REVERT: B 12 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7726 (mtt90) REVERT: B 77 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7495 (ttp80) REVERT: B 214 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8181 (mm-40) REVERT: B 349 THR cc_start: 0.8352 (m) cc_final: 0.8119 (m) REVERT: C 32 GLU cc_start: 0.6929 (mp0) cc_final: 0.6612 (mp0) REVERT: C 34 ASP cc_start: 0.7592 (m-30) cc_final: 0.7293 (m-30) REVERT: C 77 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.7469 (ttp80) REVERT: C 214 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8180 (mm-40) REVERT: C 349 THR cc_start: 0.8160 (m) cc_final: 0.7933 (m) REVERT: D 101 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7195 (mmtp) REVERT: D 367 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6373 (mt-10) REVERT: E 12 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7449 (mtt-85) REVERT: E 22 ILE cc_start: 0.8310 (pt) cc_final: 0.8039 (mm) REVERT: E 34 ASP cc_start: 0.7641 (m-30) cc_final: 0.7425 (m-30) REVERT: E 214 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8117 (mm-40) REVERT: E 324 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7806 (ttpt) REVERT: F 6 HIS cc_start: 0.8458 (m90) cc_final: 0.8247 (m-70) REVERT: F 34 ASP cc_start: 0.7561 (m-30) cc_final: 0.7353 (m-30) REVERT: F 207 ASP cc_start: 0.7768 (m-30) cc_final: 0.7521 (m-30) REVERT: F 214 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8148 (mm-40) REVERT: F 225 GLN cc_start: 0.6745 (tp40) cc_final: 0.6422 (tp40) outliers start: 0 outliers final: 1 residues processed: 559 average time/residue: 1.5325 time to fit residues: 948.2732 Evaluate side-chains 511 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 chunk 66 optimal weight: 0.2980 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 343 ASN B 24 GLN B 48 GLN B 214 GLN B 343 ASN B 347 GLN B 395 ASN C 24 GLN C 48 GLN C 137 ASN C 395 ASN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 343 ASN D 347 GLN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 48 GLN E 137 ASN E 343 ASN E 347 GLN E 395 ASN F 48 GLN F 137 ASN F 343 ASN F 347 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20622 Z= 0.155 Angle : 0.444 5.431 28008 Z= 0.239 Chirality : 0.034 0.127 3162 Planarity : 0.004 0.038 3510 Dihedral : 10.078 95.033 3084 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.39 % Allowed : 10.01 % Favored : 87.60 % 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: 1.23 (0.16), residues: 2568 helix: 1.71 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.92 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS B 116 PHE 0.011 0.001 PHE F 220 TYR 0.025 0.001 TYR B 257 ARG 0.002 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 500 time to evaluate : 2.348 Fit side-chains REVERT: A 6 HIS cc_start: 0.8596 (m90) cc_final: 0.8366 (m90) REVERT: A 22 ILE cc_start: 0.8141 (pt) cc_final: 0.7878 (mt) REVERT: B 77 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7514 (ttp80) REVERT: B 214 GLN cc_start: 0.8265 (mm110) cc_final: 0.8055 (mm-40) REVERT: B 349 THR cc_start: 0.8301 (m) cc_final: 0.8071 (m) REVERT: C 34 ASP cc_start: 0.7513 (m-30) cc_final: 0.7289 (m-30) REVERT: C 85 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7784 (tttt) REVERT: C 141 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7640 (ttpp) REVERT: C 349 THR cc_start: 0.8112 (m) cc_final: 0.7898 (m) REVERT: C 383 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7321 (mmm-85) REVERT: D 101 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7206 (mmtp) REVERT: D 367 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6260 (mt-10) REVERT: E 12 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7467 (mtt-85) REVERT: E 22 ILE cc_start: 0.8290 (pt) cc_final: 0.8046 (mm) REVERT: E 34 ASP cc_start: 0.7513 (m-30) cc_final: 0.7300 (m-30) REVERT: E 117 ASP cc_start: 0.7525 (m-30) cc_final: 0.7068 (t0) REVERT: E 214 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8059 (mm-40) REVERT: F 117 ASP cc_start: 0.7647 (m-30) cc_final: 0.7259 (t0) REVERT: F 159 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: F 214 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8089 (mm-40) outliers start: 47 outliers final: 14 residues processed: 515 average time/residue: 1.5329 time to fit residues: 873.6949 Evaluate side-chains 493 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 476 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 261 ASP 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: 6.9990 chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 343 ASN A 361 ASN B 13 GLN B 24 GLN B 48 GLN B 343 ASN B 347 GLN C 24 GLN C 48 GLN C 137 ASN C 347 GLN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 343 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 48 GLN E 137 ASN E 199 HIS E 343 ASN E 347 GLN ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 137 ASN F 343 ASN F 347 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 20622 Z= 0.587 Angle : 0.662 6.706 28008 Z= 0.358 Chirality : 0.048 0.185 3162 Planarity : 0.005 0.043 3510 Dihedral : 11.194 113.033 3084 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.05 % Allowed : 12.20 % Favored : 84.76 % 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: 0.30 (0.16), residues: 2568 helix: 0.91 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -1.13 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 240 HIS 0.011 0.003 HIS B 116 PHE 0.030 0.003 PHE F 220 TYR 0.023 0.002 TYR F 257 ARG 0.005 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 536 time to evaluate : 2.619 Fit side-chains REVERT: A 6 HIS cc_start: 0.8649 (m90) cc_final: 0.8390 (m90) REVERT: B 6 HIS cc_start: 0.8568 (m90) cc_final: 0.8224 (m-70) REVERT: B 34 ASP cc_start: 0.7628 (m-30) cc_final: 0.7353 (m-30) REVERT: B 85 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7714 (tttp) REVERT: B 263 GLU cc_start: 0.7194 (tt0) cc_final: 0.6989 (tt0) REVERT: C 32 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: C 34 ASP cc_start: 0.7773 (m-30) cc_final: 0.7507 (m-30) REVERT: C 91 TYR cc_start: 0.8294 (m-80) cc_final: 0.8007 (m-80) REVERT: C 326 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7404 (tt0) REVERT: C 349 THR cc_start: 0.8292 (m) cc_final: 0.8079 (m) REVERT: D 32 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: D 226 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 336 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: D 367 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6546 (mt-10) REVERT: E 34 ASP cc_start: 0.7731 (m-30) cc_final: 0.7521 (m-30) REVERT: E 85 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7749 (ttpt) REVERT: E 157 LYS cc_start: 0.8169 (mttm) cc_final: 0.7458 (mtpt) REVERT: E 159 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: E 254 ASP cc_start: 0.6948 (m-30) cc_final: 0.6600 (m-30) REVERT: F 150 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7978 (mttp) REVERT: F 205 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (tt) REVERT: F 207 ASP cc_start: 0.7965 (m-30) cc_final: 0.7680 (m-30) REVERT: F 214 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8073 (mm-40) REVERT: F 254 ASP cc_start: 0.6821 (m-30) cc_final: 0.6545 (m-30) REVERT: F 340 ASP cc_start: 0.6691 (m-30) cc_final: 0.6330 (m-30) REVERT: F 437 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7591 (mtpt) outliers start: 60 outliers final: 23 residues processed: 555 average time/residue: 1.4861 time to fit residues: 914.6681 Evaluate side-chains 563 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 534 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 261 ASP 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: 1.9990 chunk 176 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 112 optimal weight: 0.0670 chunk 157 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 343 ASN C 24 GLN C 137 ASN C 214 GLN C 361 ASN C 395 ASN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 343 ASN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 137 ASN E 153 GLN E 343 ASN E 395 ASN F 48 GLN F 153 GLN F 161 ASN F 199 HIS F 214 GLN F 347 GLN F 395 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20622 Z= 0.154 Angle : 0.445 6.601 28008 Z= 0.240 Chirality : 0.034 0.123 3162 Planarity : 0.004 0.045 3510 Dihedral : 9.958 100.353 3084 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.29 % Allowed : 14.33 % Favored : 83.38 % 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: 1.22 (0.16), residues: 2568 helix: 1.70 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.93 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 240 HIS 0.003 0.001 HIS B 116 PHE 0.013 0.001 PHE E 220 TYR 0.020 0.001 TYR F 257 ARG 0.003 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 494 time to evaluate : 2.541 Fit side-chains REVERT: A 6 HIS cc_start: 0.8625 (m90) cc_final: 0.8390 (m-70) REVERT: B 6 HIS cc_start: 0.8581 (m90) cc_final: 0.8258 (m-70) REVERT: B 85 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7613 (tttp) REVERT: B 263 GLU cc_start: 0.7138 (tt0) cc_final: 0.6917 (tt0) REVERT: B 349 THR cc_start: 0.8284 (m) cc_final: 0.7987 (m) REVERT: C 6 HIS cc_start: 0.8545 (m90) cc_final: 0.8251 (m-70) REVERT: C 34 ASP cc_start: 0.7574 (m-30) cc_final: 0.7347 (m-30) REVERT: C 326 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7420 (tt0) REVERT: C 383 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7334 (mmm-85) REVERT: D 226 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 367 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6268 (mt-10) REVERT: E 12 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7602 (mtt-85) REVERT: E 159 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: F 34 ASP cc_start: 0.7495 (m-30) cc_final: 0.7210 (m-30) REVERT: F 159 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: F 254 ASP cc_start: 0.6666 (m-30) cc_final: 0.6429 (m-30) REVERT: F 326 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7193 (tm-30) outliers start: 45 outliers final: 17 residues processed: 507 average time/residue: 1.5664 time to fit residues: 879.2280 Evaluate side-chains 507 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 487 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 214 GLN B 343 ASN B 347 GLN C 24 GLN C 48 GLN C 52 GLN C 137 ASN C 214 GLN C 347 GLN C 361 ASN C 395 ASN D 3 ASN D 13 GLN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 343 ASN D 347 GLN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 153 GLN E 343 ASN E 347 GLN ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 20622 Z= 0.472 Angle : 0.601 6.287 28008 Z= 0.325 Chirality : 0.044 0.172 3162 Planarity : 0.005 0.050 3510 Dihedral : 10.718 107.891 3084 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.79 % Allowed : 16.21 % Favored : 81.00 % 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: 0.54 (0.16), residues: 2568 helix: 1.13 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -1.11 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 240 HIS 0.009 0.002 HIS B 116 PHE 0.027 0.003 PHE F 220 TYR 0.022 0.002 TYR F 257 ARG 0.011 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 515 time to evaluate : 2.264 Fit side-chains REVERT: A 6 HIS cc_start: 0.8633 (m90) cc_final: 0.8366 (m90) REVERT: A 32 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: B 6 HIS cc_start: 0.8530 (m90) cc_final: 0.8189 (m-70) REVERT: B 34 ASP cc_start: 0.7532 (m-30) cc_final: 0.7260 (m-30) REVERT: B 85 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7681 (tttp) REVERT: B 263 GLU cc_start: 0.7191 (tt0) cc_final: 0.6978 (tt0) REVERT: C 6 HIS cc_start: 0.8560 (m90) cc_final: 0.8226 (m-70) REVERT: C 34 ASP cc_start: 0.7701 (m-30) cc_final: 0.7397 (m-30) REVERT: C 91 TYR cc_start: 0.8258 (m-80) cc_final: 0.7983 (m-80) REVERT: C 226 GLU cc_start: 0.7452 (tp30) cc_final: 0.7009 (tp30) REVERT: C 326 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7320 (tt0) REVERT: D 32 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: D 226 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7187 (tm-30) REVERT: D 367 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6526 (mt-10) REVERT: D 383 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7888 (mmm-85) REVERT: E 150 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7876 (mttp) REVERT: E 157 LYS cc_start: 0.8175 (mttm) cc_final: 0.7427 (mtpt) REVERT: E 159 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: E 191 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7613 (ptmt) REVERT: E 254 ASP cc_start: 0.6943 (m-30) cc_final: 0.6700 (m-30) REVERT: F 34 ASP cc_start: 0.7628 (m-30) cc_final: 0.7393 (m-30) REVERT: F 150 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7863 (mttt) REVERT: F 159 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: F 200 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8078 (mtmm) REVERT: F 205 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8175 (tt) REVERT: F 254 ASP cc_start: 0.6751 (m-30) cc_final: 0.6479 (m-30) REVERT: F 340 ASP cc_start: 0.6701 (m-30) cc_final: 0.6338 (m-30) REVERT: F 437 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7509 (mtpt) outliers start: 55 outliers final: 23 residues processed: 532 average time/residue: 1.5048 time to fit residues: 887.4163 Evaluate side-chains 552 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 520 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 343 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 214 GLN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 343 ASN C 137 ASN C 347 GLN C 361 ASN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 343 ASN D 347 GLN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 GLN E 343 ASN E 347 GLN ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20622 Z= 0.225 Angle : 0.480 6.319 28008 Z= 0.259 Chirality : 0.036 0.138 3162 Planarity : 0.004 0.045 3510 Dihedral : 10.032 100.727 3084 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.95 % Allowed : 15.85 % Favored : 81.20 % 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: 0.92 (0.16), residues: 2568 helix: 1.49 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -1.08 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 240 HIS 0.005 0.001 HIS B 116 PHE 0.018 0.002 PHE F 220 TYR 0.020 0.001 TYR C 257 ARG 0.008 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 496 time to evaluate : 2.613 Fit side-chains REVERT: A 6 HIS cc_start: 0.8626 (m90) cc_final: 0.8400 (m-70) REVERT: A 226 GLU cc_start: 0.7497 (tp30) cc_final: 0.7070 (tp30) REVERT: B 6 HIS cc_start: 0.8545 (m90) cc_final: 0.8213 (m-70) REVERT: B 34 ASP cc_start: 0.7452 (m-30) cc_final: 0.7144 (m-30) REVERT: B 85 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7634 (tttp) REVERT: B 263 GLU cc_start: 0.7113 (tt0) cc_final: 0.6900 (tt0) REVERT: B 334 PHE cc_start: 0.8427 (t80) cc_final: 0.8123 (t80) REVERT: B 345 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7441 (tp-100) REVERT: C 6 HIS cc_start: 0.8545 (m90) cc_final: 0.8231 (m-70) REVERT: C 34 ASP cc_start: 0.7607 (m-30) cc_final: 0.7314 (m-30) REVERT: C 91 TYR cc_start: 0.8211 (m-80) cc_final: 0.7931 (m-80) REVERT: C 226 GLU cc_start: 0.7513 (tp30) cc_final: 0.7124 (tp30) REVERT: C 326 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7253 (tt0) REVERT: C 401 LEU cc_start: 0.7604 (tp) cc_final: 0.7368 (tt) REVERT: D 226 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 367 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6372 (mt-10) REVERT: E 117 ASP cc_start: 0.7514 (m-30) cc_final: 0.7118 (t0) REVERT: E 159 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: E 254 ASP cc_start: 0.6891 (m-30) cc_final: 0.6630 (m-30) REVERT: E 383 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7366 (mmm160) REVERT: F 34 ASP cc_start: 0.7529 (m-30) cc_final: 0.7231 (m-30) REVERT: F 117 ASP cc_start: 0.7675 (m-30) cc_final: 0.7259 (t0) REVERT: F 150 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7892 (mttt) REVERT: F 159 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: F 205 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8149 (tt) REVERT: F 254 ASP cc_start: 0.6683 (m-30) cc_final: 0.6426 (m-30) REVERT: F 326 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7170 (tm-30) REVERT: F 437 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7499 (mtpt) outliers start: 58 outliers final: 26 residues processed: 517 average time/residue: 1.5160 time to fit residues: 868.6081 Evaluate side-chains 533 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 501 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 205 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 248 optimal weight: 0.0270 chunk 155 optimal weight: 5.9990 chunk 151 optimal weight: 0.0770 chunk 114 optimal weight: 10.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 13 GLN A 137 ASN A 343 ASN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 137 ASN B 214 GLN B 343 ASN B 347 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 347 GLN D 361 ASN D 389 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 153 GLN E 343 ASN E 347 GLN E 395 ASN F 137 ASN F 400 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20622 Z= 0.181 Angle : 0.450 7.408 28008 Z= 0.243 Chirality : 0.035 0.130 3162 Planarity : 0.004 0.040 3510 Dihedral : 9.508 96.465 3084 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.54 % Allowed : 17.17 % Favored : 80.28 % 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: 1.23 (0.16), residues: 2568 helix: 1.74 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -1.01 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 240 HIS 0.004 0.001 HIS B 116 PHE 0.015 0.001 PHE F 220 TYR 0.021 0.001 TYR B 257 ARG 0.005 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 501 time to evaluate : 2.732 Fit side-chains REVERT: A 6 HIS cc_start: 0.8625 (m90) cc_final: 0.8371 (m-70) REVERT: A 226 GLU cc_start: 0.7504 (tp30) cc_final: 0.7093 (tp30) REVERT: B 6 HIS cc_start: 0.8543 (m90) cc_final: 0.8215 (m-70) REVERT: B 85 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7657 (tttp) REVERT: B 334 PHE cc_start: 0.8392 (t80) cc_final: 0.8115 (t80) REVERT: B 349 THR cc_start: 0.8274 (m) cc_final: 0.7986 (m) REVERT: C 6 HIS cc_start: 0.8529 (m90) cc_final: 0.8212 (m-70) REVERT: C 34 ASP cc_start: 0.7516 (m-30) cc_final: 0.7291 (m-30) REVERT: C 226 GLU cc_start: 0.7542 (tp30) cc_final: 0.7201 (tp30) REVERT: C 326 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7355 (tt0) REVERT: C 401 LEU cc_start: 0.7587 (tp) cc_final: 0.7362 (tt) REVERT: D 32 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: D 226 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7131 (tm-30) REVERT: D 369 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6862 (mt-10) REVERT: E 117 ASP cc_start: 0.7532 (m-30) cc_final: 0.7112 (t0) REVERT: E 159 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: E 303 VAL cc_start: 0.8040 (t) cc_final: 0.7820 (m) REVERT: E 383 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7229 (mmm160) REVERT: F 117 ASP cc_start: 0.7617 (m-30) cc_final: 0.7183 (t0) REVERT: F 150 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7843 (mttt) REVERT: F 159 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: F 254 ASP cc_start: 0.6681 (m-30) cc_final: 0.6430 (m-30) outliers start: 50 outliers final: 23 residues processed: 522 average time/residue: 1.5305 time to fit residues: 884.4721 Evaluate side-chains 529 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 501 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 383 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 205 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.0370 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 158 optimal weight: 0.0170 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN A 137 ASN A 214 GLN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 137 ASN B 214 GLN B 343 ASN B 347 GLN C 137 ASN C 361 ASN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS E 137 ASN E 153 GLN E 161 ASN E 343 ASN E 347 GLN E 395 ASN F 137 ASN F 400 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20622 Z= 0.119 Angle : 0.408 7.656 28008 Z= 0.217 Chirality : 0.033 0.122 3162 Planarity : 0.003 0.039 3510 Dihedral : 8.598 88.967 3084 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.73 % Allowed : 18.04 % Favored : 80.23 % 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: 1.76 (0.17), residues: 2568 helix: 2.15 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.80 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 240 HIS 0.003 0.001 HIS A 116 PHE 0.008 0.001 PHE D 334 TYR 0.021 0.001 TYR E 257 ARG 0.005 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 502 time to evaluate : 2.411 Fit side-chains REVERT: A 6 HIS cc_start: 0.8606 (m90) cc_final: 0.8366 (m-70) REVERT: A 226 GLU cc_start: 0.7480 (tp30) cc_final: 0.7109 (tp30) REVERT: B 6 HIS cc_start: 0.8549 (m90) cc_final: 0.8206 (m-70) REVERT: B 85 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7621 (tttp) REVERT: B 349 THR cc_start: 0.8234 (m) cc_final: 0.7954 (m) REVERT: C 6 HIS cc_start: 0.8529 (m90) cc_final: 0.8231 (m-70) REVERT: C 117 ASP cc_start: 0.7433 (m-30) cc_final: 0.7172 (t0) REVERT: C 226 GLU cc_start: 0.7547 (tp30) cc_final: 0.7257 (tp30) REVERT: C 401 LEU cc_start: 0.7540 (tp) cc_final: 0.7328 (tt) REVERT: D 226 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7133 (tm-30) REVERT: D 369 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6649 (mt-10) REVERT: E 117 ASP cc_start: 0.7509 (m-30) cc_final: 0.7153 (t0) REVERT: E 159 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: F 117 ASP cc_start: 0.7576 (m-30) cc_final: 0.7247 (t0) REVERT: F 150 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7947 (mttt) REVERT: F 159 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: F 214 GLN cc_start: 0.8255 (mm110) cc_final: 0.7978 (mm-40) outliers start: 34 outliers final: 16 residues processed: 515 average time/residue: 1.5342 time to fit residues: 875.0954 Evaluate side-chains 509 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 490 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 205 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 137 ASN B 214 GLN B 343 ASN B 347 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 137 ASN E 153 GLN E 343 ASN E 347 GLN E 395 ASN F 48 GLN F 52 GLN F 137 ASN F 347 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20622 Z= 0.174 Angle : 0.446 7.366 28008 Z= 0.240 Chirality : 0.035 0.133 3162 Planarity : 0.004 0.039 3510 Dihedral : 8.909 86.534 3084 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.63 % Allowed : 19.05 % Favored : 79.32 % 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: 1.67 (0.16), residues: 2568 helix: 2.07 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.80 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 240 HIS 0.005 0.001 HIS A 116 PHE 0.016 0.001 PHE F 220 TYR 0.022 0.001 TYR B 257 ARG 0.007 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 495 time to evaluate : 2.491 Fit side-chains REVERT: A 6 HIS cc_start: 0.8621 (m90) cc_final: 0.8374 (m-70) REVERT: A 226 GLU cc_start: 0.7512 (tp30) cc_final: 0.7113 (tp30) REVERT: B 6 HIS cc_start: 0.8559 (m90) cc_final: 0.8198 (m-70) REVERT: B 85 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7671 (tttp) REVERT: B 345 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7562 (mm110) REVERT: B 349 THR cc_start: 0.8264 (m) cc_final: 0.7997 (m) REVERT: C 6 HIS cc_start: 0.8523 (m90) cc_final: 0.8208 (m-70) REVERT: C 117 ASP cc_start: 0.7357 (m-30) cc_final: 0.7072 (t0) REVERT: C 155 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 226 GLU cc_start: 0.7556 (tp30) cc_final: 0.7228 (tp30) REVERT: C 401 LEU cc_start: 0.7609 (tp) cc_final: 0.7368 (tt) REVERT: C 437 LYS cc_start: 0.8005 (tppp) cc_final: 0.7774 (mtmm) REVERT: D 226 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 369 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6873 (mt-10) REVERT: E 117 ASP cc_start: 0.7465 (m-30) cc_final: 0.7072 (t0) REVERT: E 159 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: F 117 ASP cc_start: 0.7594 (m-30) cc_final: 0.7163 (t0) REVERT: F 150 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7945 (mttt) REVERT: F 159 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: F 214 GLN cc_start: 0.8257 (mm110) cc_final: 0.7978 (mm-40) outliers start: 32 outliers final: 21 residues processed: 510 average time/residue: 1.5325 time to fit residues: 864.6041 Evaluate side-chains 514 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 489 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 343 ASN C 24 GLN C 48 GLN C 214 GLN C 347 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 214 GLN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 HIS E 137 ASN E 153 GLN E 343 ASN E 347 GLN E 395 ASN F 137 ASN F 347 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20622 Z= 0.262 Angle : 0.501 6.856 28008 Z= 0.271 Chirality : 0.037 0.147 3162 Planarity : 0.004 0.039 3510 Dihedral : 9.588 85.275 3084 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.83 % Allowed : 19.51 % Favored : 78.66 % 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 (0.16), residues: 2568 helix: 1.74 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -0.95 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 240 HIS 0.006 0.002 HIS A 116 PHE 0.021 0.002 PHE F 220 TYR 0.022 0.002 TYR F 257 ARG 0.005 0.000 ARG B 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 512 time to evaluate : 2.312 Fit side-chains REVERT: A 6 HIS cc_start: 0.8630 (m90) cc_final: 0.8375 (m-70) REVERT: A 32 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: A 226 GLU cc_start: 0.7537 (tp30) cc_final: 0.7104 (tp30) REVERT: B 6 HIS cc_start: 0.8539 (m90) cc_final: 0.8191 (m-70) REVERT: B 85 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7643 (tttp) REVERT: C 6 HIS cc_start: 0.8534 (m90) cc_final: 0.8207 (m-70) REVERT: C 137 ASN cc_start: 0.7824 (m-40) cc_final: 0.7599 (m-40) REVERT: C 226 GLU cc_start: 0.7527 (tp30) cc_final: 0.7155 (tp30) REVERT: C 326 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7223 (tt0) REVERT: D 32 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: D 226 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7201 (tm-30) REVERT: E 117 ASP cc_start: 0.7443 (m-30) cc_final: 0.6998 (t0) REVERT: E 159 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: F 117 ASP cc_start: 0.7596 (m-30) cc_final: 0.7127 (t0) REVERT: F 150 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7942 (mttt) REVERT: F 159 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: F 205 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 214 GLN cc_start: 0.8263 (mm110) cc_final: 0.8037 (mm-40) outliers start: 36 outliers final: 19 residues processed: 527 average time/residue: 1.5611 time to fit residues: 909.2788 Evaluate side-chains 541 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 516 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 437 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 24 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 343 ASN A 347 GLN A 361 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 343 ASN C 24 GLN C 48 GLN C 214 GLN C 347 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 24 GLN D 48 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 153 GLN E 343 ASN E 347 GLN E 393 HIS ** E 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN F 347 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101029 restraints weight = 25628.087| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.45 r_work: 0.3131 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20622 Z= 0.390 Angle : 0.571 6.924 28008 Z= 0.309 Chirality : 0.041 0.169 3162 Planarity : 0.004 0.040 3510 Dihedral : 9.985 88.002 3084 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.73 % Allowed : 19.26 % Favored : 79.01 % 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: 0.86 (0.16), residues: 2568 helix: 1.41 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -1.02 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 240 HIS 0.008 0.002 HIS B 116 PHE 0.023 0.002 PHE F 220 TYR 0.023 0.002 TYR F 257 ARG 0.006 0.000 ARG D 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11640.32 seconds wall clock time: 208 minutes 35.85 seconds (12515.85 seconds total)