Starting phenix.real_space_refine on Sat Feb 17 14:50:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/02_2024/7rys_24747_updated.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6124 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8528 2.51 5 N 2080 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "B" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "C" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 7.33, per 1000 atoms: 0.57 Number of scatterers: 12900 At special positions: 0 Unit cell: (108.009, 108.009, 113.464, 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 28 16.00 P 8 15.00 O 2256 8.00 N 2080 7.00 C 8528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 55.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.109A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.998A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 112' Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.735A pdb=" N ALA A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.949A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.220A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.543A pdb=" N VAL A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.722A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.587A pdb=" N GLU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'B' and resid 12 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.110A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.999A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 112' Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.735A pdb=" N ALA B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.949A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 224 removed outlier: 4.220A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.543A pdb=" N VAL B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.721A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.586A pdb=" N GLU B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'C' and resid 12 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.109A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.997A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 112' Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.735A pdb=" N ALA C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.949A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 157 " --> pdb=" O CYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 224 removed outlier: 4.219A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.543A pdb=" N VAL C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.721A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.587A pdb=" N GLU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 312 No H-bonds generated for 'chain 'C' and resid 309 through 312' Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'D' and resid 12 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.109A pdb=" N LEU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.997A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 112' Processing helix chain 'D' and resid 115 through 123 removed outlier: 4.736A pdb=" N ALA D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.949A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 224 removed outlier: 4.220A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.543A pdb=" N VAL D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.721A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.587A pdb=" N GLU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 405 through 417 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.536A pdb=" N TYR A 390 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE A 341 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 392 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A 339 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 346 through 349 removed outlier: 4.202A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.537A pdb=" N TYR B 390 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE B 341 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 392 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 339 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 346 through 349 removed outlier: 4.201A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 318 through 322 removed outlier: 6.536A pdb=" N TYR C 390 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE C 341 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU C 392 " --> pdb=" O TYR C 339 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C 339 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 346 through 349 removed outlier: 4.202A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.536A pdb=" N TYR D 390 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE D 341 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU D 392 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR D 339 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 346 through 349 removed outlier: 4.201A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1632 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: 3.43 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2043 1.32 - 1.44: 3259 1.44 - 1.57: 7790 1.57 - 1.69: 16 1.69 - 1.81: 48 Bond restraints: 13156 Sorted by residual: bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" C GLY B 332 " pdb=" N GLU B 333 " ideal model delta sigma weight residual 1.330 1.424 -0.094 1.38e-02 5.25e+03 4.61e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 95.07 - 103.27: 149 103.27 - 111.47: 5761 111.47 - 119.67: 6013 119.67 - 127.87: 5756 127.87 - 136.07: 117 Bond angle restraints: 17796 Sorted by residual: angle pdb=" N TYR C 259 " pdb=" CA TYR C 259 " pdb=" C TYR C 259 " ideal model delta sigma weight residual 111.14 104.24 6.90 1.08e+00 8.57e-01 4.08e+01 angle pdb=" N TYR D 259 " pdb=" CA TYR D 259 " pdb=" C TYR D 259 " ideal model delta sigma weight residual 111.14 104.25 6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N TYR A 259 " pdb=" CA TYR A 259 " pdb=" C TYR A 259 " ideal model delta sigma weight residual 111.14 104.26 6.88 1.08e+00 8.57e-01 4.06e+01 angle pdb=" N TYR B 259 " pdb=" CA TYR B 259 " pdb=" C TYR B 259 " ideal model delta sigma weight residual 111.14 104.30 6.84 1.08e+00 8.57e-01 4.01e+01 angle pdb=" N LEU A 98 " pdb=" CA LEU A 98 " pdb=" C LEU A 98 " ideal model delta sigma weight residual 113.19 106.71 6.48 1.19e+00 7.06e-01 2.97e+01 ... (remaining 17791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 7800 34.90 - 69.79: 172 69.79 - 104.69: 8 104.69 - 139.58: 24 139.58 - 174.48: 8 Dihedral angle restraints: 8012 sinusoidal: 3444 harmonic: 4568 Sorted by residual: dihedral pdb=" C07 PGW B 503 " pdb=" C06 PGW B 503 " pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.42 174.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW C 503 " pdb=" C06 PGW C 503 " pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.39 174.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW A 503 " pdb=" C06 PGW A 503 " pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.39 174.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1443 0.048 - 0.096: 462 0.096 - 0.144: 107 0.144 - 0.192: 44 0.192 - 0.240: 28 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CA LEU C 98 " pdb=" N LEU C 98 " pdb=" C LEU C 98 " pdb=" CB LEU C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU A 98 " pdb=" N LEU A 98 " pdb=" C LEU A 98 " pdb=" CB LEU A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LEU B 98 " pdb=" N LEU B 98 " pdb=" C LEU B 98 " pdb=" CB LEU B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2081 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 503 " -0.067 2.00e-02 2.50e+03 6.68e-02 4.47e+01 pdb=" C10 PGW C 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW C 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW C 503 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.067 2.00e-02 2.50e+03 6.68e-02 4.46e+01 pdb=" C10 PGW A 503 " -0.067 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.067 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " -0.067 2.00e-02 2.50e+03 6.67e-02 4.45e+01 pdb=" C10 PGW B 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " 0.066 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2428 2.78 - 3.31: 12435 3.31 - 3.84: 19650 3.84 - 4.37: 22735 4.37 - 4.90: 38996 Nonbonded interactions: 96244 Sorted by model distance: nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.254 2.440 ... (remaining 96239 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 group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 3.590 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.600 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.007 0.176 13156 Z= 0.478 Angle : 1.112 12.890 17796 Z= 0.654 Chirality : 0.056 0.240 2084 Planarity : 0.008 0.067 2156 Dihedral : 18.240 174.480 5060 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.30 % Allowed : 1.80 % Favored : 97.90 % 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: -1.42 (0.21), residues: 1532 helix: -0.45 (0.17), residues: 936 sheet: -1.24 (0.42), residues: 112 loop : -1.61 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 264 HIS 0.007 0.002 HIS D 232 PHE 0.030 0.003 PHE D 340 TYR 0.014 0.002 TYR A 259 ARG 0.010 0.001 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.558 Fit side-chains REVERT: A 229 LYS cc_start: 0.8680 (tptt) cc_final: 0.8464 (tptt) REVERT: A 261 ASP cc_start: 0.7486 (t70) cc_final: 0.7195 (t0) REVERT: B 261 ASP cc_start: 0.7680 (t70) cc_final: 0.7390 (t0) REVERT: C 261 ASP cc_start: 0.7734 (t70) cc_final: 0.7444 (t0) REVERT: D 341 ILE cc_start: 0.8245 (mm) cc_final: 0.8039 (mm) outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.2840 time to fit residues: 89.2594 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 88 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 253 GLN B 131 ASN B 253 GLN B 364 GLN C 131 ASN C 253 GLN D 131 ASN D 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13156 Z= 0.161 Angle : 0.673 8.113 17796 Z= 0.311 Chirality : 0.041 0.179 2084 Planarity : 0.005 0.050 2156 Dihedral : 16.594 151.752 2112 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.60 % Allowed : 10.29 % Favored : 89.11 % 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: -0.71 (0.22), residues: 1532 helix: 0.11 (0.18), residues: 968 sheet: -1.83 (0.36), residues: 124 loop : -1.07 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.005 0.001 HIS D 232 PHE 0.019 0.001 PHE D 365 TYR 0.012 0.001 TYR D 357 ARG 0.004 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.360 Fit side-chains REVERT: A 103 PRO cc_start: 0.6878 (Cg_endo) cc_final: 0.6675 (Cg_exo) REVERT: A 261 ASP cc_start: 0.7633 (t70) cc_final: 0.7324 (t0) REVERT: B 261 ASP cc_start: 0.7736 (t70) cc_final: 0.7390 (t0) REVERT: B 277 LYS cc_start: 0.8018 (mttm) cc_final: 0.7695 (pttt) REVERT: C 261 ASP cc_start: 0.7763 (t70) cc_final: 0.7466 (t0) REVERT: C 277 LYS cc_start: 0.7891 (mttm) cc_final: 0.7617 (pttt) REVERT: D 210 MET cc_start: 0.6623 (mpp) cc_final: 0.6188 (mpp) REVERT: D 342 ASN cc_start: 0.8569 (t0) cc_final: 0.8273 (t0) outliers start: 8 outliers final: 5 residues processed: 195 average time/residue: 0.2847 time to fit residues: 76.7119 Evaluate side-chains 170 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain D residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS B 253 GLN B 364 GLN C 99 HIS D 99 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13156 Z= 0.189 Angle : 0.640 8.121 17796 Z= 0.296 Chirality : 0.040 0.153 2084 Planarity : 0.004 0.049 2156 Dihedral : 14.929 130.249 2112 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.05 % Allowed : 13.14 % Favored : 85.81 % 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: -0.49 (0.22), residues: 1532 helix: 0.41 (0.18), residues: 952 sheet: -1.96 (0.36), residues: 124 loop : -1.21 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS A 232 PHE 0.016 0.001 PHE D 365 TYR 0.011 0.001 TYR D 175 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.519 Fit side-chains REVERT: A 103 PRO cc_start: 0.6906 (Cg_endo) cc_final: 0.6687 (Cg_exo) REVERT: A 114 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7986 (ttmm) REVERT: A 210 MET cc_start: 0.6585 (mtt) cc_final: 0.6174 (mpp) REVERT: A 261 ASP cc_start: 0.7664 (t70) cc_final: 0.7314 (t0) REVERT: A 277 LYS cc_start: 0.8219 (pttt) cc_final: 0.7209 (mttm) REVERT: A 343 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7165 (ttp80) REVERT: B 114 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7955 (mttp) REVERT: B 210 MET cc_start: 0.6535 (mtt) cc_final: 0.6209 (mpp) REVERT: B 261 ASP cc_start: 0.7727 (t70) cc_final: 0.7352 (t0) REVERT: B 273 ARG cc_start: 0.7365 (ptt90) cc_final: 0.7144 (mpp-170) REVERT: C 261 ASP cc_start: 0.7705 (t70) cc_final: 0.7341 (t0) outliers start: 14 outliers final: 8 residues processed: 180 average time/residue: 0.2922 time to fit residues: 72.7160 Evaluate side-chains 162 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 140 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 0.0170 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS D 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13156 Z= 0.238 Angle : 0.643 8.133 17796 Z= 0.300 Chirality : 0.041 0.138 2084 Planarity : 0.004 0.048 2156 Dihedral : 13.136 130.134 2112 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.50 % Allowed : 15.39 % Favored : 83.11 % 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: -0.38 (0.22), residues: 1532 helix: 0.49 (0.18), residues: 948 sheet: -1.82 (0.36), residues: 132 loop : -1.15 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 15 HIS 0.003 0.001 HIS C 149 PHE 0.016 0.001 PHE B 397 TYR 0.012 0.001 TYR B 175 ARG 0.005 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.520 Fit side-chains REVERT: A 114 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8050 (ttmm) REVERT: A 261 ASP cc_start: 0.7694 (t70) cc_final: 0.7336 (t0) REVERT: A 277 LYS cc_start: 0.8176 (pttt) cc_final: 0.7312 (mttm) REVERT: B 261 ASP cc_start: 0.7720 (t70) cc_final: 0.7328 (t0) REVERT: B 273 ARG cc_start: 0.7397 (ptt90) cc_final: 0.7126 (mpp-170) REVERT: C 261 ASP cc_start: 0.7750 (t70) cc_final: 0.7355 (t0) REVERT: C 277 LYS cc_start: 0.7896 (mttm) cc_final: 0.7577 (ptmt) REVERT: D 206 LEU cc_start: 0.8157 (tp) cc_final: 0.7931 (tp) outliers start: 20 outliers final: 15 residues processed: 178 average time/residue: 0.2794 time to fit residues: 69.9692 Evaluate side-chains 169 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13156 Z= 0.227 Angle : 0.643 8.125 17796 Z= 0.298 Chirality : 0.041 0.132 2084 Planarity : 0.004 0.047 2156 Dihedral : 12.266 130.055 2112 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.43 % Allowed : 17.79 % Favored : 80.78 % 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: -0.26 (0.22), residues: 1532 helix: 0.55 (0.18), residues: 956 sheet: -1.78 (0.37), residues: 132 loop : -1.01 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 15 HIS 0.002 0.001 HIS A 281 PHE 0.029 0.001 PHE B 397 TYR 0.011 0.001 TYR B 175 ARG 0.005 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.553 Fit side-chains REVERT: A 261 ASP cc_start: 0.7744 (t70) cc_final: 0.7388 (t0) REVERT: B 261 ASP cc_start: 0.7724 (t70) cc_final: 0.7332 (t0) REVERT: B 273 ARG cc_start: 0.7383 (ptt90) cc_final: 0.7106 (mpp-170) REVERT: B 343 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7540 (ttm110) REVERT: C 261 ASP cc_start: 0.7757 (t70) cc_final: 0.7352 (t0) outliers start: 19 outliers final: 17 residues processed: 170 average time/residue: 0.2624 time to fit residues: 64.2718 Evaluate side-chains 164 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13156 Z= 0.276 Angle : 0.658 8.123 17796 Z= 0.308 Chirality : 0.042 0.131 2084 Planarity : 0.004 0.047 2156 Dihedral : 11.652 129.926 2112 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.73 % 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: -0.28 (0.22), residues: 1532 helix: 0.57 (0.18), residues: 952 sheet: -1.84 (0.37), residues: 132 loop : -1.11 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 15 HIS 0.003 0.001 HIS B 149 PHE 0.032 0.001 PHE B 397 TYR 0.012 0.001 TYR A 175 ARG 0.006 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 1.460 Fit side-chains REVERT: A 261 ASP cc_start: 0.7703 (t70) cc_final: 0.7324 (t0) REVERT: B 261 ASP cc_start: 0.7737 (t70) cc_final: 0.7357 (t0) REVERT: C 261 ASP cc_start: 0.7735 (t70) cc_final: 0.7307 (t0) REVERT: D 210 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6321 (mpp) outliers start: 36 outliers final: 24 residues processed: 176 average time/residue: 0.2469 time to fit residues: 63.3122 Evaluate side-chains 172 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 83 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13156 Z= 0.160 Angle : 0.637 9.571 17796 Z= 0.290 Chirality : 0.040 0.136 2084 Planarity : 0.004 0.046 2156 Dihedral : 11.063 130.138 2112 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.58 % Allowed : 19.22 % Favored : 79.20 % 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: 0.00 (0.23), residues: 1532 helix: 0.82 (0.18), residues: 948 sheet: -1.71 (0.38), residues: 132 loop : -1.05 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 176 HIS 0.002 0.001 HIS A 99 PHE 0.018 0.001 PHE B 397 TYR 0.008 0.001 TYR A 170 ARG 0.006 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7711 (t70) cc_final: 0.7378 (t0) REVERT: B 261 ASP cc_start: 0.7704 (t70) cc_final: 0.7354 (t0) REVERT: C 261 ASP cc_start: 0.7750 (t70) cc_final: 0.7375 (t0) REVERT: D 210 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6573 (mpp) outliers start: 21 outliers final: 13 residues processed: 169 average time/residue: 0.2465 time to fit residues: 60.5915 Evaluate side-chains 161 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13156 Z= 0.207 Angle : 0.644 8.964 17796 Z= 0.294 Chirality : 0.040 0.134 2084 Planarity : 0.004 0.045 2156 Dihedral : 10.977 130.089 2112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.80 % Allowed : 19.67 % Favored : 78.53 % 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: 0.02 (0.23), residues: 1532 helix: 0.79 (0.18), residues: 952 sheet: -1.62 (0.39), residues: 132 loop : -0.97 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 15 HIS 0.002 0.001 HIS D 149 PHE 0.015 0.001 PHE B 397 TYR 0.010 0.001 TYR C 175 ARG 0.007 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.606 Fit side-chains REVERT: A 261 ASP cc_start: 0.7687 (t70) cc_final: 0.7334 (t0) REVERT: A 334 MET cc_start: 0.4351 (tpp) cc_final: 0.4111 (tpp) REVERT: B 261 ASP cc_start: 0.7705 (t70) cc_final: 0.7351 (t0) REVERT: B 343 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7581 (ttm110) REVERT: C 261 ASP cc_start: 0.7750 (t70) cc_final: 0.7375 (t0) REVERT: D 210 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6499 (mpp) outliers start: 24 outliers final: 18 residues processed: 167 average time/residue: 0.2519 time to fit residues: 62.2662 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13156 Z= 0.187 Angle : 0.649 12.733 17796 Z= 0.294 Chirality : 0.040 0.137 2084 Planarity : 0.004 0.045 2156 Dihedral : 10.818 130.134 2112 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.88 % Allowed : 19.52 % Favored : 78.60 % 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: 0.09 (0.23), residues: 1532 helix: 0.87 (0.18), residues: 944 sheet: -1.56 (0.40), residues: 132 loop : -0.97 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.002 0.001 HIS D 232 PHE 0.012 0.001 PHE A 397 TYR 0.009 0.001 TYR C 175 ARG 0.007 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7694 (t70) cc_final: 0.7383 (t0) REVERT: B 261 ASP cc_start: 0.7682 (t70) cc_final: 0.7326 (t0) REVERT: C 261 ASP cc_start: 0.7692 (t70) cc_final: 0.7321 (t0) REVERT: D 210 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6496 (mpp) outliers start: 25 outliers final: 21 residues processed: 164 average time/residue: 0.2440 time to fit residues: 58.4249 Evaluate side-chains 171 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 0.0000 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 0.0470 chunk 12 optimal weight: 0.2980 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.0020 chunk 128 optimal weight: 0.9990 overall best weight: 0.1690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13156 Z= 0.144 Angle : 0.653 12.516 17796 Z= 0.289 Chirality : 0.039 0.137 2084 Planarity : 0.004 0.045 2156 Dihedral : 10.559 130.216 2112 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.58 % Allowed : 19.37 % Favored : 79.05 % 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: 0.28 (0.23), residues: 1532 helix: 1.00 (0.18), residues: 944 sheet: -1.48 (0.41), residues: 132 loop : -0.89 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 176 HIS 0.001 0.000 HIS C 232 PHE 0.011 0.001 PHE D 397 TYR 0.008 0.001 TYR D 357 ARG 0.008 0.000 ARG A 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7670 (t70) cc_final: 0.7426 (t0) REVERT: B 261 ASP cc_start: 0.7673 (t70) cc_final: 0.7372 (t0) REVERT: C 261 ASP cc_start: 0.7666 (t70) cc_final: 0.7360 (t0) REVERT: C 334 MET cc_start: 0.4798 (tpp) cc_final: 0.4555 (tpp) REVERT: D 210 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6269 (mpp) outliers start: 21 outliers final: 18 residues processed: 166 average time/residue: 0.2615 time to fit residues: 62.0313 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.211077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.192070 restraints weight = 14590.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.189816 restraints weight = 19089.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188973 restraints weight = 22113.842| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13156 Z= 0.166 Angle : 0.662 12.020 17796 Z= 0.296 Chirality : 0.040 0.136 2084 Planarity : 0.004 0.045 2156 Dihedral : 10.527 130.210 2112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.65 % Allowed : 19.89 % Favored : 78.45 % 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: 0.32 (0.23), residues: 1532 helix: 1.01 (0.18), residues: 944 sheet: -1.42 (0.41), residues: 132 loop : -0.83 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 264 HIS 0.001 0.001 HIS D 232 PHE 0.011 0.001 PHE D 397 TYR 0.007 0.001 TYR A 175 ARG 0.008 0.000 ARG B 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.16 seconds wall clock time: 43 minutes 58.91 seconds (2638.91 seconds total)