Starting phenix.real_space_refine on Thu Mar 14 23:07:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g13_29660/03_2024/8g13_29660.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6316 2.51 5 N 1736 2.21 5 O 1896 1.98 5 H 12 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 141": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10008 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2502 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2502 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2502 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2502 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.62, per 1000 atoms: 0.56 Number of scatterers: 10008 At special positions: 0 Unit cell: (94.355, 99.365, 91.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1896 8.00 N 1736 7.00 C 6316 6.00 H 12 1.00 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: 3.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 39.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.998A pdb=" N GLN B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 114' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 317 through 335 Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 114' Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.552A pdb=" N ALA C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 109 through 114' Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.721A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 317 through 335 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.551A pdb=" N ALA D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.999A pdb=" N GLN D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 114' Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.722A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 317 through 335 Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 119 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS B 179 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 240 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS B 179 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 240 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.106A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 119 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A 179 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 240 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A 179 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 240 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS C 179 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 240 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS C 179 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL C 240 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 10.105A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 119 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS D 179 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL D 240 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.577A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS D 179 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL D 240 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1368 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: 3.05 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 8 1.05 - 1.24: 1364 1.24 - 1.43: 2899 1.43 - 1.62: 5853 1.62 - 1.81: 84 Bond restraints: 10208 Sorted by residual: bond pdb=" CA CYS D 152 " pdb=" HA CYS D 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS B 152 " pdb=" HA CYS B 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS C 152 " pdb=" HA CYS C 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA CYS A 152 " pdb=" HA CYS A 152 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N VAL C 188 " pdb=" CA VAL C 188 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 10203 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.15: 301 107.15 - 113.89: 5907 113.89 - 120.63: 3998 120.63 - 127.37: 3566 127.37 - 134.11: 92 Bond angle restraints: 13864 Sorted by residual: angle pdb=" C ALA B 150 " pdb=" CA ALA B 150 " pdb=" CB ALA B 150 " ideal model delta sigma weight residual 116.63 110.36 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" C ALA C 150 " pdb=" CA ALA C 150 " pdb=" CB ALA C 150 " ideal model delta sigma weight residual 116.63 110.39 6.24 1.16e+00 7.43e-01 2.89e+01 angle pdb=" C ALA A 150 " pdb=" CA ALA A 150 " pdb=" CB ALA A 150 " ideal model delta sigma weight residual 116.63 110.40 6.23 1.16e+00 7.43e-01 2.88e+01 angle pdb=" C ALA D 150 " pdb=" CA ALA D 150 " pdb=" CB ALA D 150 " ideal model delta sigma weight residual 116.63 110.42 6.21 1.16e+00 7.43e-01 2.87e+01 angle pdb=" N ARG A 80 " pdb=" CA ARG A 80 " pdb=" C ARG A 80 " ideal model delta sigma weight residual 113.41 108.74 4.67 1.22e+00 6.72e-01 1.46e+01 ... (remaining 13859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5375 17.09 - 34.19: 461 34.19 - 51.28: 147 51.28 - 68.38: 33 68.38 - 85.47: 8 Dihedral angle restraints: 6024 sinusoidal: 2248 harmonic: 3776 Sorted by residual: dihedral pdb=" CG ARG D 197 " pdb=" CD ARG D 197 " pdb=" NE ARG D 197 " pdb=" CZ ARG D 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.92 42.92 2 1.50e+01 4.44e-03 9.89e+00 dihedral pdb=" CG ARG C 197 " pdb=" CD ARG C 197 " pdb=" NE ARG C 197 " pdb=" CZ ARG C 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.91 42.91 2 1.50e+01 4.44e-03 9.89e+00 dihedral pdb=" CG ARG A 197 " pdb=" CD ARG A 197 " pdb=" NE ARG A 197 " pdb=" CZ ARG A 197 " ideal model delta sinusoidal sigma weight residual -90.00 -132.91 42.91 2 1.50e+01 4.44e-03 9.89e+00 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1078 0.041 - 0.081: 315 0.081 - 0.122: 167 0.122 - 0.163: 12 0.163 - 0.203: 8 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA VAL B 188 " pdb=" N VAL B 188 " pdb=" C VAL B 188 " pdb=" CB VAL B 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL A 188 " pdb=" N VAL A 188 " pdb=" C VAL A 188 " pdb=" CB VAL A 188 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1577 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 268 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 269 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 269 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 268 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 269 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " -0.018 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.59: 76 2.59 - 3.09: 7050 3.09 - 3.59: 11331 3.59 - 4.10: 17078 4.10 - 4.60: 25617 Nonbonded interactions: 61152 Sorted by model distance: nonbonded pdb=" NH2 ARG A 118 " pdb=" OD1 ASN A 142 " model vdw 2.083 2.350 nonbonded pdb=" NH2 ARG B 118 " pdb=" OD1 ASN B 142 " model vdw 2.083 2.350 nonbonded pdb=" NH2 ARG C 118 " pdb=" OD1 ASN C 142 " model vdw 2.083 2.350 nonbonded pdb=" NH2 ARG D 118 " pdb=" OD1 ASN D 142 " model vdw 2.083 2.350 nonbonded pdb=" NZ LYS D 3 " pdb=" O GLY D 26 " model vdw 2.288 2.350 ... (remaining 61147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 3.380 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.340 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 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 : 0.004 0.039 10196 Z= 0.288 Angle : 0.597 6.272 13832 Z= 0.407 Chirality : 0.049 0.203 1580 Planarity : 0.003 0.032 1796 Dihedral : 14.969 85.473 3612 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.86 % Allowed : 13.21 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.25), residues: 1328 helix: 2.33 (0.26), residues: 368 sheet: 0.27 (0.38), residues: 212 loop : -0.10 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 313 HIS 0.003 0.001 HIS A 137 PHE 0.007 0.001 PHE B 318 TYR 0.007 0.001 TYR D 314 ARG 0.002 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.080 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 1.4632 time to fit residues: 146.4964 Evaluate side-chains 77 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 0.0170 chunk 119 optimal weight: 7.9990 overall best weight: 2.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN B 185 GLN A 149 ASN A 185 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 10196 Z= 0.213 Angle : 0.463 6.160 13832 Z= 0.263 Chirality : 0.044 0.130 1580 Planarity : 0.004 0.045 1796 Dihedral : 4.482 28.019 1420 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.38 % Allowed : 15.40 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1328 helix: 2.44 (0.27), residues: 372 sheet: -0.41 (0.35), residues: 232 loop : -0.20 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.003 0.001 HIS D 137 PHE 0.010 0.001 PHE D 286 TYR 0.012 0.001 TYR B 42 ARG 0.008 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.917 Fit side-chains REVERT: B 223 GLU cc_start: 0.8471 (mp0) cc_final: 0.8235 (mp0) REVERT: A 223 GLU cc_start: 0.8469 (mp0) cc_final: 0.8232 (mp0) REVERT: C 223 GLU cc_start: 0.8469 (mp0) cc_final: 0.8232 (mp0) REVERT: D 223 GLU cc_start: 0.8470 (mp0) cc_final: 0.8236 (mp0) outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 1.5469 time to fit residues: 118.5837 Evaluate side-chains 68 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10196 Z= 0.296 Angle : 0.490 6.522 13832 Z= 0.277 Chirality : 0.046 0.142 1580 Planarity : 0.004 0.041 1796 Dihedral : 4.145 14.836 1412 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.43 % Allowed : 14.16 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.25), residues: 1328 helix: 2.14 (0.27), residues: 372 sheet: -0.65 (0.32), residues: 288 loop : -0.04 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 87 HIS 0.003 0.001 HIS B 53 PHE 0.012 0.001 PHE C 318 TYR 0.011 0.002 TYR C 314 ARG 0.007 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.219 Fit side-chains REVERT: B 223 GLU cc_start: 0.8494 (mp0) cc_final: 0.8245 (mp0) REVERT: A 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8244 (mp0) REVERT: C 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8246 (mp0) REVERT: D 223 GLU cc_start: 0.8493 (mp0) cc_final: 0.8248 (mp0) outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 1.5043 time to fit residues: 126.6527 Evaluate side-chains 72 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10196 Z= 0.241 Angle : 0.459 6.294 13832 Z= 0.259 Chirality : 0.045 0.133 1580 Planarity : 0.004 0.042 1796 Dihedral : 4.041 15.933 1412 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.81 % Allowed : 13.97 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.25), residues: 1328 helix: 2.24 (0.27), residues: 372 sheet: -0.65 (0.32), residues: 288 loop : -0.06 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 313 HIS 0.003 0.001 HIS B 137 PHE 0.008 0.001 PHE D 286 TYR 0.010 0.001 TYR C 314 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 1.137 Fit side-chains REVERT: B 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8234 (mp0) REVERT: A 223 GLU cc_start: 0.8481 (mp0) cc_final: 0.8234 (mp0) REVERT: C 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8236 (mp0) REVERT: D 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8236 (mp0) outliers start: 19 outliers final: 8 residues processed: 83 average time/residue: 1.3668 time to fit residues: 121.4485 Evaluate side-chains 72 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 10196 Z= 0.167 Angle : 0.424 5.723 13832 Z= 0.238 Chirality : 0.043 0.123 1580 Planarity : 0.004 0.040 1796 Dihedral : 3.835 16.105 1412 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.95 % Allowed : 14.45 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.25), residues: 1328 helix: 2.48 (0.27), residues: 372 sheet: -0.67 (0.31), residues: 288 loop : 0.05 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 313 HIS 0.002 0.000 HIS B 137 PHE 0.006 0.001 PHE D 286 TYR 0.008 0.001 TYR D 314 ARG 0.008 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.237 Fit side-chains REVERT: B 223 GLU cc_start: 0.8474 (mp0) cc_final: 0.8231 (mp0) REVERT: A 223 GLU cc_start: 0.8470 (mp0) cc_final: 0.8226 (mp0) REVERT: C 223 GLU cc_start: 0.8470 (mp0) cc_final: 0.8227 (mp0) REVERT: D 223 GLU cc_start: 0.8475 (mp0) cc_final: 0.8229 (mp0) outliers start: 10 outliers final: 4 residues processed: 74 average time/residue: 1.5869 time to fit residues: 125.0639 Evaluate side-chains 68 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 10196 Z= 0.310 Angle : 0.487 6.694 13832 Z= 0.274 Chirality : 0.046 0.146 1580 Planarity : 0.004 0.042 1796 Dihedral : 4.099 16.864 1412 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.95 % Allowed : 14.07 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.25), residues: 1328 helix: 2.21 (0.26), residues: 372 sheet: -0.69 (0.32), residues: 288 loop : -0.04 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 87 HIS 0.003 0.001 HIS B 137 PHE 0.010 0.001 PHE A 286 TYR 0.011 0.001 TYR D 314 ARG 0.008 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.216 Fit side-chains REVERT: B 223 GLU cc_start: 0.8488 (mp0) cc_final: 0.8240 (mp0) REVERT: A 223 GLU cc_start: 0.8486 (mp0) cc_final: 0.8235 (mp0) REVERT: C 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8232 (mp0) REVERT: D 223 GLU cc_start: 0.8485 (mp0) cc_final: 0.8235 (mp0) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 1.5431 time to fit residues: 121.6695 Evaluate side-chains 72 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 10196 Z= 0.243 Angle : 0.460 6.265 13832 Z= 0.258 Chirality : 0.045 0.131 1580 Planarity : 0.004 0.044 1796 Dihedral : 4.037 17.639 1412 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.05 % Allowed : 13.97 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.25), residues: 1328 helix: 2.30 (0.27), residues: 372 sheet: -0.71 (0.31), residues: 288 loop : -0.05 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 313 HIS 0.003 0.001 HIS C 137 PHE 0.009 0.001 PHE C 286 TYR 0.010 0.001 TYR D 314 ARG 0.009 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.173 Fit side-chains REVERT: B 223 GLU cc_start: 0.8482 (mp0) cc_final: 0.8236 (mp0) REVERT: A 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8234 (mp0) REVERT: C 223 GLU cc_start: 0.8478 (mp0) cc_final: 0.8234 (mp0) REVERT: D 223 GLU cc_start: 0.8479 (mp0) cc_final: 0.8234 (mp0) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 1.6119 time to fit residues: 128.5889 Evaluate side-chains 72 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 10196 Z= 0.425 Angle : 0.540 7.277 13832 Z= 0.303 Chirality : 0.048 0.165 1580 Planarity : 0.004 0.048 1796 Dihedral : 4.299 17.986 1412 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.81 % Allowed : 13.31 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.24), residues: 1328 helix: 1.97 (0.26), residues: 372 sheet: -0.71 (0.32), residues: 288 loop : -0.17 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 87 HIS 0.003 0.001 HIS B 53 PHE 0.012 0.002 PHE D 286 TYR 0.013 0.002 TYR D 314 ARG 0.010 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 1.125 Fit side-chains REVERT: B 223 GLU cc_start: 0.8487 (mp0) cc_final: 0.8240 (mp0) REVERT: A 223 GLU cc_start: 0.8487 (mp0) cc_final: 0.8242 (mp0) REVERT: C 223 GLU cc_start: 0.8492 (mp0) cc_final: 0.8245 (mp0) REVERT: D 223 GLU cc_start: 0.8494 (mp0) cc_final: 0.8245 (mp0) outliers start: 19 outliers final: 16 residues processed: 79 average time/residue: 1.5557 time to fit residues: 131.4603 Evaluate side-chains 80 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 244 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 10196 Z= 0.260 Angle : 0.475 6.583 13832 Z= 0.267 Chirality : 0.045 0.140 1580 Planarity : 0.004 0.049 1796 Dihedral : 4.122 18.037 1412 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.14 % Allowed : 13.97 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.24), residues: 1328 helix: 2.13 (0.26), residues: 372 sheet: -0.73 (0.31), residues: 288 loop : -0.13 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 313 HIS 0.003 0.001 HIS B 137 PHE 0.009 0.001 PHE D 286 TYR 0.010 0.001 TYR D 314 ARG 0.011 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.232 Fit side-chains REVERT: B 223 GLU cc_start: 0.8490 (mp0) cc_final: 0.8241 (mp0) REVERT: A 223 GLU cc_start: 0.8490 (mp0) cc_final: 0.8241 (mp0) REVERT: C 223 GLU cc_start: 0.8495 (mp0) cc_final: 0.8246 (mp0) REVERT: D 223 GLU cc_start: 0.8497 (mp0) cc_final: 0.8248 (mp0) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 1.5636 time to fit residues: 126.7033 Evaluate side-chains 76 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 0.0170 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10196 Z= 0.145 Angle : 0.419 5.462 13832 Z= 0.235 Chirality : 0.043 0.125 1580 Planarity : 0.004 0.050 1796 Dihedral : 3.860 17.395 1412 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.14 % Allowed : 14.16 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1328 helix: 2.41 (0.27), residues: 372 sheet: -0.69 (0.31), residues: 288 loop : 0.01 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 313 HIS 0.002 0.000 HIS B 137 PHE 0.005 0.001 PHE D 286 TYR 0.007 0.001 TYR D 314 ARG 0.011 0.001 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.095 Fit side-chains REVERT: B 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8238 (mp0) REVERT: A 223 GLU cc_start: 0.8480 (mp0) cc_final: 0.8238 (mp0) REVERT: C 223 GLU cc_start: 0.8468 (mp0) cc_final: 0.8228 (mp0) REVERT: D 223 GLU cc_start: 0.8462 (mp0) cc_final: 0.8224 (mp0) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 1.5449 time to fit residues: 125.7033 Evaluate side-chains 76 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.0570 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.064346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.051200 restraints weight = 19628.666| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.50 r_work: 0.2527 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10196 Z= 0.160 Angle : 0.425 5.651 13832 Z= 0.237 Chirality : 0.043 0.124 1580 Planarity : 0.004 0.056 1796 Dihedral : 3.796 16.741 1412 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.76 % Allowed : 14.64 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.25), residues: 1328 helix: 2.52 (0.27), residues: 372 sheet: -0.60 (0.31), residues: 288 loop : 0.07 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS C 137 PHE 0.006 0.001 PHE C 286 TYR 0.007 0.001 TYR C 314 ARG 0.013 0.001 ARG C 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.50 seconds wall clock time: 55 minutes 23.73 seconds (3323.73 seconds total)