Starting phenix.real_space_refine on Fri May 10 05:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v30_42939/05_2024/8v30_42939_neut_updated.pdb" } resolution = 2.54 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9405 2.51 5 N 2495 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 107": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2899 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.71, per 1000 atoms: 0.52 Number of scatterers: 14910 At special positions: 0 Unit cell: (79.92, 104.76, 194.4, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 2880 8.00 N 2495 7.00 C 9405 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 2.7 seconds 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 20 sheets defined 41.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.721A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.323A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.845A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.743A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.243A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.877A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.761A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 194 removed outlier: 4.180A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.938A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.731A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.968A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.904A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.126A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.748A pdb=" N SER E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.259A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.899A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 5.076A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.699A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.729A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.493A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.791A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.499A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.781A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.468A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.766A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.468A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.783A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.450A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 516 hydrogen bonds defined for protein. 1341 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: 4.35 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 2480 1.32 - 1.46: 5021 1.46 - 1.60: 7539 1.60 - 1.74: 15 1.74 - 1.89: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" C CYS G 5 " pdb=" N HYP G 6 " ideal model delta sigma weight residual 1.329 1.490 -0.161 1.40e-02 5.10e+03 1.32e+02 bond pdb=" C CYS H 5 " pdb=" N HYP H 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.31e+02 bond pdb=" C CYS J 5 " pdb=" N HYP J 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.31e+02 bond pdb=" C CYS F 5 " pdb=" N HYP F 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.30e+02 bond pdb=" C CYS I 5 " pdb=" N HYP I 6 " ideal model delta sigma weight residual 1.329 1.489 -0.160 1.40e-02 5.10e+03 1.30e+02 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.33: 393 105.33 - 113.04: 8164 113.04 - 120.76: 7046 120.76 - 128.47: 4976 128.47 - 136.18: 131 Bond angle restraints: 20710 Sorted by residual: angle pdb=" CA CYS F 5 " pdb=" C CYS F 5 " pdb=" N HYP F 6 " ideal model delta sigma weight residual 116.20 132.35 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA CYS J 5 " pdb=" C CYS J 5 " pdb=" N HYP J 6 " ideal model delta sigma weight residual 116.20 132.35 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA CYS H 5 " pdb=" C CYS H 5 " pdb=" N HYP H 6 " ideal model delta sigma weight residual 116.20 132.34 -16.14 2.00e+00 2.50e-01 6.51e+01 angle pdb=" CA CYS G 5 " pdb=" C CYS G 5 " pdb=" N HYP G 6 " ideal model delta sigma weight residual 116.20 132.28 -16.08 2.00e+00 2.50e-01 6.47e+01 angle pdb=" CA CYS I 5 " pdb=" C CYS I 5 " pdb=" N HYP I 6 " ideal model delta sigma weight residual 116.20 132.19 -15.99 2.00e+00 2.50e-01 6.39e+01 ... (remaining 20705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 8727 27.39 - 54.79: 412 54.79 - 82.18: 21 82.18 - 109.57: 0 109.57 - 136.96: 5 Dihedral angle restraints: 9165 sinusoidal: 3700 harmonic: 5465 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 76.97 -136.96 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.39 -133.39 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.31 -133.30 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1641 0.046 - 0.092: 443 0.092 - 0.138: 197 0.138 - 0.185: 13 0.185 - 0.231: 6 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA EEP J 2 " pdb=" N EEP J 2 " pdb=" C EEP J 2 " pdb=" CB EEP J 2 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA EEP G 2 " pdb=" N EEP G 2 " pdb=" C EEP G 2 " pdb=" CB EEP G 2 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA EEP I 2 " pdb=" N EEP I 2 " pdb=" C EEP I 2 " pdb=" CB EEP I 2 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2297 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 354 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" CD GLN A 354 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLN A 354 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN A 354 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 243 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 243 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.028 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 10 2.16 - 2.85: 4925 2.85 - 3.53: 18643 3.53 - 4.22: 36325 4.22 - 4.90: 63128 Nonbonded interactions: 123031 Sorted by model distance: nonbonded pdb=" N TRP F 1 " pdb=" C ALA F 7 " model vdw 1.476 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.476 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.476 3.350 nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.477 3.350 nonbonded pdb=" N TRP G 1 " pdb=" C ALA G 7 " model vdw 1.477 3.350 ... (remaining 123026 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 4 through 375) selection = (chain 'B' and resid 4 through 375) selection = (chain 'C' and resid 4 through 375) selection = (chain 'D' and resid 4 through 375) selection = (chain 'E' and resid 4 through 375) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.220 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 41.160 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.009 0.161 15245 Z= 0.570 Angle : 0.942 16.151 20710 Z= 0.488 Chirality : 0.050 0.231 2300 Planarity : 0.006 0.051 2635 Dihedral : 14.965 136.963 5665 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.51 % Allowed : 9.49 % Favored : 90.00 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 1835 helix: -1.49 (0.15), residues: 785 sheet: 0.67 (0.29), residues: 370 loop : -0.50 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 356 HIS 0.003 0.001 HIS A 161 PHE 0.017 0.002 PHE C 255 TYR 0.008 0.001 TYR E 306 ARG 0.005 0.000 ARG E 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.712 Fit side-chains REVERT: A 49 GLN cc_start: 0.8195 (mt0) cc_final: 0.7982 (mt0) REVERT: E 41 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8589 (mp10) outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 1.7309 time to fit residues: 200.8418 Evaluate side-chains 104 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15245 Z= 0.374 Angle : 0.683 10.848 20710 Z= 0.316 Chirality : 0.050 0.344 2300 Planarity : 0.004 0.035 2635 Dihedral : 8.786 119.051 2180 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.14 % Allowed : 8.23 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.09 (0.20), residues: 1835 helix: -0.21 (0.18), residues: 790 sheet: 0.76 (0.28), residues: 360 loop : -0.09 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.006 0.001 HIS B 161 PHE 0.012 0.001 PHE E 127 TYR 0.008 0.001 TYR C 306 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.720 Fit side-chains REVERT: A 41 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8927 (mp10) REVERT: A 176 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: A 314 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: B 50 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8695 (mtmm) REVERT: E 314 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8008 (tt0) outliers start: 18 outliers final: 5 residues processed: 102 average time/residue: 1.8132 time to fit residues: 200.1448 Evaluate side-chains 105 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15245 Z= 0.332 Angle : 0.632 7.532 20710 Z= 0.294 Chirality : 0.048 0.281 2300 Planarity : 0.003 0.034 2635 Dihedral : 7.359 92.292 2175 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 8.54 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.33 (0.20), residues: 1835 helix: 0.32 (0.19), residues: 785 sheet: 0.68 (0.28), residues: 360 loop : 0.07 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.005 0.001 HIS C 161 PHE 0.013 0.001 PHE C 255 TYR 0.007 0.001 TYR E 69 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.560 Fit side-chains REVERT: A 41 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8950 (mp10) REVERT: A 49 GLN cc_start: 0.8615 (mt0) cc_final: 0.8286 (mt0) REVERT: A 305 MET cc_start: 0.9302 (mmm) cc_final: 0.9064 (mmm) REVERT: A 314 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: B 314 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7581 (tp40) REVERT: C 41 GLN cc_start: 0.8845 (tp40) cc_final: 0.8517 (mp10) REVERT: C 314 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: E 314 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8007 (tt0) outliers start: 17 outliers final: 5 residues processed: 105 average time/residue: 1.8310 time to fit residues: 207.8056 Evaluate side-chains 105 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15245 Z= 0.146 Angle : 0.556 7.335 20710 Z= 0.253 Chirality : 0.044 0.262 2300 Planarity : 0.003 0.031 2635 Dihedral : 6.575 73.571 2175 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.82 % Allowed : 9.81 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.77 (0.21), residues: 1835 helix: 0.67 (0.20), residues: 785 sheet: 1.06 (0.30), residues: 325 loop : 0.26 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 356 HIS 0.003 0.000 HIS A 161 PHE 0.010 0.001 PHE C 255 TYR 0.008 0.001 TYR D 69 ARG 0.001 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.741 Fit side-chains REVERT: A 41 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8941 (mp10) REVERT: A 44 MET cc_start: -0.0531 (OUTLIER) cc_final: -0.1367 (pmt) REVERT: A 49 GLN cc_start: 0.8631 (mt0) cc_final: 0.7851 (mt0) REVERT: A 305 MET cc_start: 0.9312 (mmm) cc_final: 0.9079 (mmm) REVERT: A 314 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: C 41 GLN cc_start: 0.8892 (tp40) cc_final: 0.8441 (mp10) REVERT: C 49 GLN cc_start: 0.8179 (mt0) cc_final: 0.7960 (mt0) REVERT: E 314 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7865 (tt0) outliers start: 13 outliers final: 1 residues processed: 106 average time/residue: 1.8089 time to fit residues: 207.2825 Evaluate side-chains 105 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 152 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 246 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15245 Z= 0.423 Angle : 0.647 6.540 20710 Z= 0.303 Chirality : 0.050 0.263 2300 Planarity : 0.003 0.031 2635 Dihedral : 6.839 81.607 2175 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.89 % Allowed : 9.75 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.66 (0.21), residues: 1835 helix: 0.70 (0.20), residues: 790 sheet: 0.64 (0.29), residues: 345 loop : 0.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 1 HIS 0.006 0.001 HIS B 161 PHE 0.013 0.001 PHE A 127 TYR 0.010 0.001 TYR C 169 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.833 Fit side-chains REVERT: A 41 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8946 (mp10) REVERT: A 49 GLN cc_start: 0.8534 (mt0) cc_final: 0.8009 (mt0) REVERT: A 305 MET cc_start: 0.9324 (mmm) cc_final: 0.9085 (mmm) REVERT: A 314 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 314 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: C 41 GLN cc_start: 0.8904 (tp40) cc_final: 0.8470 (mp10) REVERT: C 49 GLN cc_start: 0.8123 (mt0) cc_final: 0.7910 (mt0) REVERT: D 314 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8138 (tp40) REVERT: E 314 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8028 (tt0) outliers start: 14 outliers final: 5 residues processed: 105 average time/residue: 1.7438 time to fit residues: 198.0966 Evaluate side-chains 107 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15245 Z= 0.311 Angle : 0.607 6.314 20710 Z= 0.283 Chirality : 0.047 0.255 2300 Planarity : 0.003 0.030 2635 Dihedral : 6.694 79.488 2175 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.01 % Allowed : 10.06 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.05 (0.21), residues: 1835 helix: 1.08 (0.20), residues: 750 sheet: 0.95 (0.29), residues: 335 loop : 0.35 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 1 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 255 TYR 0.007 0.001 TYR C 169 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.774 Fit side-chains REVERT: A 41 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8937 (mp10) REVERT: A 44 MET cc_start: -0.0880 (OUTLIER) cc_final: -0.1559 (pmt) REVERT: A 49 GLN cc_start: 0.8619 (mt0) cc_final: 0.7975 (mt0) REVERT: A 305 MET cc_start: 0.9330 (mmm) cc_final: 0.9089 (mmm) REVERT: A 314 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: B 314 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: C 41 GLN cc_start: 0.8895 (tp40) cc_final: 0.8479 (mp10) REVERT: D 314 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: E 314 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7997 (tt0) outliers start: 16 outliers final: 6 residues processed: 108 average time/residue: 1.7154 time to fit residues: 200.8546 Evaluate side-chains 108 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15245 Z= 0.337 Angle : 0.617 6.683 20710 Z= 0.288 Chirality : 0.048 0.259 2300 Planarity : 0.003 0.031 2635 Dihedral : 6.694 80.042 2175 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.95 % Allowed : 9.81 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.06 (0.21), residues: 1835 helix: 1.05 (0.20), residues: 760 sheet: 1.01 (0.30), residues: 305 loop : 0.39 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 1 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.001 PHE A 127 TYR 0.006 0.001 TYR E 69 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.795 Fit side-chains REVERT: A 49 GLN cc_start: 0.8637 (mt0) cc_final: 0.8115 (mt0) REVERT: A 305 MET cc_start: 0.9362 (mmm) cc_final: 0.9148 (mmm) REVERT: A 314 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: B 49 GLN cc_start: 0.8515 (mt0) cc_final: 0.8287 (mt0) REVERT: B 314 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: C 41 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: C 51 ASP cc_start: 0.9176 (m-30) cc_final: 0.8849 (p0) REVERT: D 51 ASP cc_start: 0.9117 (m-30) cc_final: 0.8853 (p0) REVERT: D 314 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: E 314 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8002 (tt0) outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 1.7136 time to fit residues: 196.9529 Evaluate side-chains 111 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 354 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15245 Z= 0.244 Angle : 0.586 7.087 20710 Z= 0.271 Chirality : 0.046 0.233 2300 Planarity : 0.003 0.031 2635 Dihedral : 6.498 76.934 2175 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.89 % Allowed : 10.13 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.17 (0.21), residues: 1835 helix: 1.18 (0.20), residues: 750 sheet: 0.96 (0.29), residues: 335 loop : 0.45 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 1 HIS 0.004 0.001 HIS E 161 PHE 0.010 0.001 PHE C 255 TYR 0.007 0.001 TYR E 69 ARG 0.001 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 1.447 Fit side-chains REVERT: A 49 GLN cc_start: 0.8604 (mt0) cc_final: 0.8170 (mt0) REVERT: A 305 MET cc_start: 0.9361 (mmm) cc_final: 0.9132 (mmm) REVERT: A 314 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: B 314 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: C 41 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: C 51 ASP cc_start: 0.9145 (m-30) cc_final: 0.8787 (p0) REVERT: D 51 ASP cc_start: 0.9119 (m-30) cc_final: 0.8851 (OUTLIER) REVERT: D 314 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8143 (tp40) REVERT: E 314 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7960 (tt0) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 1.7431 time to fit residues: 202.0173 Evaluate side-chains 108 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 157 optimal weight: 0.0770 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 246 GLN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15245 Z= 0.135 Angle : 0.550 9.370 20710 Z= 0.250 Chirality : 0.043 0.183 2300 Planarity : 0.003 0.031 2635 Dihedral : 6.063 65.519 2175 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.63 % Allowed : 10.51 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.36 (0.21), residues: 1835 helix: 1.26 (0.20), residues: 755 sheet: 1.02 (0.29), residues: 335 loop : 0.67 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.003 0.000 HIS A 161 PHE 0.009 0.001 PHE C 255 TYR 0.007 0.001 TYR D 69 ARG 0.001 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.694 Fit side-chains REVERT: A 49 GLN cc_start: 0.8728 (mt0) cc_final: 0.8405 (mt0) REVERT: A 305 MET cc_start: 0.9342 (mmm) cc_final: 0.9096 (mmm) REVERT: A 314 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 314 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: C 41 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: C 51 ASP cc_start: 0.9130 (m-30) cc_final: 0.8814 (p0) REVERT: D 51 ASP cc_start: 0.9083 (m-30) cc_final: 0.8834 (OUTLIER) REVERT: E 314 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7804 (tt0) outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 1.8338 time to fit residues: 211.8959 Evaluate side-chains 109 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 122 optimal weight: 0.6980 chunk 184 optimal weight: 0.0870 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 89 optimal weight: 0.0770 chunk 116 optimal weight: 0.0980 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 173 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15245 Z= 0.122 Angle : 0.536 10.376 20710 Z= 0.240 Chirality : 0.042 0.144 2300 Planarity : 0.003 0.031 2635 Dihedral : 5.495 50.825 2175 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.38 % Allowed : 10.70 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 1.45 (0.21), residues: 1835 helix: 1.37 (0.21), residues: 760 sheet: 0.79 (0.29), residues: 370 loop : 0.83 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.002 0.000 HIS B 40 PHE 0.008 0.001 PHE D 255 TYR 0.007 0.000 TYR E 69 ARG 0.001 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3670 Ramachandran restraints generated. 1835 Oldfield, 0 Emsley, 1835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.772 Fit side-chains REVERT: A 49 GLN cc_start: 0.8654 (mt0) cc_final: 0.8288 (mt0) REVERT: C 41 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: C 51 ASP cc_start: 0.9135 (m-30) cc_final: 0.8816 (p0) REVERT: C 246 GLN cc_start: 0.8506 (mt0) cc_final: 0.8279 (mt0) REVERT: D 51 ASP cc_start: 0.9077 (m-30) cc_final: 0.8828 (OUTLIER) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 1.7232 time to fit residues: 201.5494 Evaluate side-chains 106 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain E residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.053781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.042762 restraints weight = 35379.041| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 2.59 r_work: 0.2331 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2202 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15245 Z= 0.171 Angle : 0.547 9.915 20710 Z= 0.246 Chirality : 0.043 0.156 2300 Planarity : 0.003 0.030 2635 Dihedral : 5.554 54.663 2175 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.32 % Allowed : 11.27 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1835 helix: 1.34 (0.21), residues: 760 sheet: 0.80 (0.29), residues: 370 loop : 0.84 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 1 HIS 0.003 0.000 HIS E 161 PHE 0.009 0.001 PHE C 255 TYR 0.005 0.001 TYR E 69 ARG 0.002 0.000 ARG C 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.21 seconds wall clock time: 77 minutes 37.40 seconds (4657.40 seconds total)