Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 05:14:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_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_26129/10_2023/7tu8_26129_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_26129_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu8_26129/10_2023/7tu8_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 10.79, per 1000 atoms: 0.53 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: 8.10 Conformation dependent library (CDL) restraints added in 2.9 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: 3.43 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: 5.72 Time building geometry restraints manager: 8.74 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: 11567 23.57 - 47.15: 445 47.15 - 70.72: 75 70.72 - 94.30: 15 94.30 - 117.87: 6 Dihedral angle restraints: 12108 sinusoidal: 4524 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 12105 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.010 Extract box with map and model: 3.730 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 52.550 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.560 ------------------------------------------------------------------------------- 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 : 13.323 117.871 7248 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 *********************** 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 : 2.292 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 559 average time/residue: 1.5423 time to fit residues: 954.8596 Evaluate side-chains 508 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2200 time to fit residues: 3.4044 ------------------------------------------------------------------------------- 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: 0.9990 chunk 108 optimal weight: 0.0170 chunk 66 optimal weight: 0.2980 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 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 214 GLN F 343 ASN F 347 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20622 Z= 0.138 Angle : 0.435 5.528 28008 Z= 0.234 Chirality : 0.033 0.121 3162 Planarity : 0.004 0.038 3510 Dihedral : 6.099 97.612 2886 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.34 % Allowed : 10.57 % Favored : 87.09 % 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: 1.30 (0.16), residues: 2568 helix: 1.77 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.91 (0.20), residues: 888 *********************** 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 539 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 493 time to evaluate : 2.067 Fit side-chains outliers start: 46 outliers final: 9 residues processed: 506 average time/residue: 1.5547 time to fit residues: 871.0544 Evaluate side-chains 480 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 471 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 1.0597 time to fit residues: 10.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 13 GLN B 24 GLN B 48 GLN B 214 GLN B 343 ASN B 347 GLN C 24 GLN C 48 GLN C 137 ASN C 347 GLN C 395 ASN 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 13 GLN F 48 GLN F 343 ASN F 347 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20622 Z= 0.403 Angle : 0.571 6.347 28008 Z= 0.309 Chirality : 0.042 0.165 3162 Planarity : 0.004 0.041 3510 Dihedral : 6.487 106.631 2886 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.90 % Allowed : 12.75 % Favored : 84.35 % 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: 0.74 (0.16), residues: 2568 helix: 1.29 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -1.03 (0.20), residues: 888 *********************** 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 576 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 519 time to evaluate : 2.228 Fit side-chains outliers start: 57 outliers final: 20 residues processed: 537 average time/residue: 1.5191 time to fit residues: 906.2001 Evaluate side-chains 525 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 505 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 5 residues processed: 15 average time/residue: 0.2942 time to fit residues: 9.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 48 GLN B 199 HIS B 214 GLN B 343 ASN B 347 GLN C 24 GLN C 137 ASN C 214 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 48 GLN E 137 ASN E 153 GLN E 343 ASN E 347 GLN E 395 ASN F 48 GLN F 137 ASN F 153 GLN F 199 HIS F 347 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1813 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= 0.160 Angle : 0.442 6.638 28008 Z= 0.238 Chirality : 0.034 0.127 3162 Planarity : 0.004 0.043 3510 Dihedral : 5.866 97.997 2886 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.13 % Allowed : 14.84 % Favored : 83.03 % 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: 1.24 (0.16), residues: 2568 helix: 1.75 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -1.00 (0.20), residues: 888 *********************** 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 530 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 488 time to evaluate : 2.237 Fit side-chains outliers start: 42 outliers final: 13 residues processed: 501 average time/residue: 1.5797 time to fit residues: 876.5916 Evaluate side-chains 493 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 480 time to evaluate : 2.246 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.4502 time to fit residues: 6.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.0270 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 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: 2.9990 chunk 223 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 1.4842 ------------------------------------------------------------------------------- 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 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 214 GLN B 343 ASN B 347 GLN C 137 ASN C 345 GLN C 347 GLN D 3 ASN D 24 GLN D 48 GLN D 137 ASN 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 48 GLN F 137 ASN F 153 GLN F 347 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20622 Z= 0.242 Angle : 0.485 6.250 28008 Z= 0.261 Chirality : 0.037 0.145 3162 Planarity : 0.004 0.040 3510 Dihedral : 5.858 97.797 2886 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 16.11 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2568 helix: 1.67 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -1.00 (0.20), residues: 894 *********************** 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 542 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 494 time to evaluate : 2.383 Fit side-chains outliers start: 48 outliers final: 20 residues processed: 511 average time/residue: 1.5890 time to fit residues: 900.5941 Evaluate side-chains 510 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 490 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 8 residues processed: 12 average time/residue: 0.4525 time to fit residues: 10.4927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 207 optimal weight: 0.0470 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.2092 ------------------------------------------------------------------------------- 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 347 GLN D 3 ASN D 24 GLN D 48 GLN D 137 ASN D 343 ASN D 347 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 395 ASN F 13 GLN F 48 GLN F 137 ASN F 153 GLN F 347 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20622 Z= 0.207 Angle : 0.466 6.727 28008 Z= 0.251 Chirality : 0.036 0.138 3162 Planarity : 0.004 0.039 3510 Dihedral : 5.689 95.343 2886 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.88 % Allowed : 16.87 % Favored : 81.25 % 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: 1.24 (0.16), residues: 2568 helix: 1.75 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.99 (0.20), residues: 888 *********************** 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 530 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 493 time to evaluate : 2.427 Fit side-chains outliers start: 37 outliers final: 14 residues processed: 508 average time/residue: 1.5354 time to fit residues: 865.0534 Evaluate side-chains 504 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 490 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.6630 time to fit residues: 7.0323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 114 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 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 D 3 ASN D 13 GLN 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 137 ASN E 153 GLN E 343 ASN E 347 GLN E 395 ASN F 48 GLN F 137 ASN F 153 GLN F 214 GLN F 347 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.005 0.050 20622 Z= 0.347 Angle : 0.546 6.242 28008 Z= 0.295 Chirality : 0.040 0.160 3162 Planarity : 0.004 0.040 3510 Dihedral : 5.947 97.255 2886 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 17.23 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2568 helix: 1.45 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -1.04 (0.20), residues: 894 *********************** 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 556 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 519 time to evaluate : 2.250 Fit side-chains outliers start: 37 outliers final: 19 residues processed: 534 average time/residue: 1.5733 time to fit residues: 930.3124 Evaluate side-chains 531 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 512 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 10 average time/residue: 0.3605 time to fit residues: 8.5545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 158 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 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 D 3 ASN D 13 GLN D 24 GLN D 48 GLN D 137 ASN D 361 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 153 GLN E 343 ASN E 347 GLN F 48 GLN F 137 ASN F 153 GLN F 214 GLN F 347 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2104 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= 0.143 Angle : 0.441 7.462 28008 Z= 0.235 Chirality : 0.034 0.120 3162 Planarity : 0.003 0.040 3510 Dihedral : 5.367 88.776 2886 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.17 % Allowed : 18.24 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2568 helix: 1.95 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.87 (0.20), residues: 888 *********************** 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 515 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 492 time to evaluate : 2.188 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 505 average time/residue: 1.5834 time to fit residues: 885.9098 Evaluate side-chains 496 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 486 time to evaluate : 2.261 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 2 average time/residue: 0.2740 time to fit residues: 4.3349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 152 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: