Starting phenix.real_space_refine on Mon Dec 11 23:00:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtj_24682/12_2023/7rtj_24682_updated.pdb" } resolution = 3.8 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= 0.003 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 8860 2.51 5 N 2140 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13352 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "D" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3170 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 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: 57 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 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: 57 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 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: 57 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 266 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: 57 Time building chain proxies: 7.05, per 1000 atoms: 0.53 Number of scatterers: 13352 At special positions: 0 Unit cell: (106.937, 106.937, 114.348, 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 2316 8.00 N 2140 7.00 C 8860 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: 4.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 59.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 102 through 124 removed outlier: 5.032A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.725A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 223 removed outlier: 3.710A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.701A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 281 through 298 removed outlier: 6.158A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.932A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'B' and resid 13 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 95 through 98 No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 102 through 124 removed outlier: 5.032A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.725A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 223 removed outlier: 3.711A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.702A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 281 through 298 removed outlier: 6.159A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.932A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'C' and resid 13 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 95 through 98 No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 102 through 124 removed outlier: 5.032A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 Processing helix chain 'C' and resid 166 through 181 removed outlier: 3.725A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 3.710A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.702A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 266 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 281 through 298 removed outlier: 6.159A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.932A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 405 through 419 Processing helix chain 'D' and resid 13 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 102 through 124 removed outlier: 5.032A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.725A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 223 removed outlier: 3.710A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.701A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 266 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 281 through 298 removed outlier: 6.158A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.932A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 405 through 419 Processing sheet with id= A, first strand: chain 'A' and resid 346 through 349 Processing sheet with id= B, first strand: chain 'A' and resid 338 through 343 removed outlier: 3.839A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 392 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 390 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 346 through 349 Processing sheet with id= D, first strand: chain 'B' and resid 338 through 343 removed outlier: 3.838A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 392 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 390 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 346 through 349 Processing sheet with id= F, first strand: chain 'C' and resid 338 through 343 removed outlier: 3.838A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 392 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 390 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 346 through 349 Processing sheet with id= H, first strand: chain 'D' and resid 338 through 343 removed outlier: 3.839A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 392 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 390 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1836 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: 3.71 Time building geometry restraints manager: 5.16 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: 2088 1.32 - 1.44: 3376 1.44 - 1.56: 8084 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13616 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW A 505 " pdb=" C9 PGW A 505 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 ... (remaining 13611 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.91: 475 106.91 - 113.75: 7744 113.75 - 120.59: 5708 120.59 - 127.43: 4293 127.43 - 134.27: 164 Bond angle restraints: 18384 Sorted by residual: angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 112.54 106.05 6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 112.54 106.06 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 112.54 106.11 6.43 1.22e+00 6.72e-01 2.78e+01 angle pdb=" C10 PGW D 507 " pdb=" C9 PGW D 507 " pdb=" C8 PGW D 507 " ideal model delta sigma weight residual 127.02 112.18 14.84 3.00e+00 1.11e-01 2.45e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 7824 31.75 - 63.50: 472 63.50 - 95.26: 20 95.26 - 127.01: 16 127.01 - 158.76: 12 Dihedral angle restraints: 8344 sinusoidal: 3664 harmonic: 4680 Sorted by residual: dihedral pdb=" C5' CMP D 503 " pdb=" O5' CMP D 503 " pdb=" P CMP D 503 " pdb=" O1P CMP D 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.67 -112.67 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' CMP B 503 " pdb=" O5' CMP B 503 " pdb=" P CMP B 503 " pdb=" O1P CMP B 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.64 -112.64 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" C5' CMP C 503 " pdb=" O5' CMP C 503 " pdb=" P CMP C 503 " pdb=" O1P CMP C 503 " ideal model delta sinusoidal sigma weight residual 60.00 172.62 -112.62 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1560 0.052 - 0.104: 447 0.104 - 0.157: 113 0.157 - 0.209: 8 0.209 - 0.261: 12 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CA PRO C 405 " pdb=" N PRO C 405 " pdb=" C PRO C 405 " pdb=" CB PRO C 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO D 405 " pdb=" N PRO D 405 " pdb=" C PRO D 405 " pdb=" CB PRO D 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 405 " pdb=" N PRO B 405 " pdb=" C PRO B 405 " pdb=" CB PRO B 405 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2137 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " 0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW D 504 " -0.148 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " 0.142 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 504 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW B 504 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW B 504 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW B 504 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " -0.144 2.00e-02 2.50e+03 1.43e-01 2.03e+02 pdb=" C10 PGW A 502 " 0.148 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.142 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.137 2.00e-02 2.50e+03 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2071 2.76 - 3.29: 12964 3.29 - 3.83: 21955 3.83 - 4.36: 23891 4.36 - 4.90: 42060 Nonbonded interactions: 102941 Sorted by model distance: nonbonded pdb=" O ARG D 417 " pdb=" NH1 ARG D 417 " model vdw 2.224 2.520 nonbonded pdb=" O ARG A 417 " pdb=" NH1 ARG A 417 " model vdw 2.224 2.520 nonbonded pdb=" O ARG C 417 " pdb=" NH1 ARG C 417 " model vdw 2.224 2.520 nonbonded pdb=" O ARG B 417 " pdb=" NH1 ARG B 417 " model vdw 2.225 2.520 nonbonded pdb=" O ILE C 178 " pdb=" OG1 THR C 182 " model vdw 2.253 2.440 ... (remaining 102936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or (resid 506 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name C5 or name C \ 6 or name O01 or name O02 or name O03 or name O04)) or (resid 508 and (name C01 \ or name C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C \ 18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or n \ ame C5 or name C6 or name O01 or name O02 or name O03 or name O04)) or resid 509 \ )) selection = (chain 'B' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) selection = (chain 'D' and (resid 10 through 420 or (resid 504 and (name C3 or name C4 or na \ me C5 or name C6 )) or resid 506 or (resid 508 and (name C01 or name C02 or name \ C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C3 or name C4 or name C5 or name C6 o \ r name O01 or name O02 or name O03 or name O04)) or (resid 509 and (name C15 or \ name C16 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27)))) } 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: 0.720 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: 3.490 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 35.050 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.008 0.190 13616 Z= 0.544 Angle : 1.025 14.836 18384 Z= 0.508 Chirality : 0.053 0.261 2140 Planarity : 0.008 0.143 2224 Dihedral : 20.090 158.761 5320 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.17 % Allowed : 26.17 % Favored : 72.66 % 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 (0.22), residues: 1576 helix: 0.39 (0.17), residues: 1028 sheet: 0.95 (0.65), residues: 96 loop : -0.90 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 264 HIS 0.004 0.001 HIS D 149 PHE 0.009 0.002 PHE A 302 TYR 0.012 0.001 TYR B 175 ARG 0.004 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 1.435 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 288 average time/residue: 0.2275 time to fit residues: 96.7948 Evaluate side-chains 274 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13616 Z= 0.189 Angle : 0.621 9.276 18384 Z= 0.290 Chirality : 0.041 0.129 2140 Planarity : 0.005 0.063 2224 Dihedral : 17.114 159.166 2288 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.29 % Allowed : 26.32 % Favored : 70.39 % 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: 0.21 (0.22), residues: 1576 helix: 0.58 (0.17), residues: 1028 sheet: 1.04 (0.66), residues: 88 loop : -0.87 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 264 HIS 0.002 0.001 HIS A 149 PHE 0.006 0.001 PHE A 302 TYR 0.010 0.001 TYR D 175 ARG 0.002 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 261 time to evaluate : 1.484 Fit side-chains outliers start: 45 outliers final: 20 residues processed: 277 average time/residue: 0.2384 time to fit residues: 98.1251 Evaluate side-chains 272 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1150 time to fit residues: 6.2098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.0370 chunk 117 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 0.0040 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13616 Z= 0.168 Angle : 0.616 8.322 18384 Z= 0.286 Chirality : 0.040 0.129 2140 Planarity : 0.004 0.057 2224 Dihedral : 15.818 143.851 2288 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.80 % Allowed : 25.07 % Favored : 71.13 % 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: 0.66 (0.23), residues: 1576 helix: 0.85 (0.17), residues: 1016 sheet: 0.78 (0.62), residues: 88 loop : -0.34 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.001 0.001 HIS A 149 PHE 0.007 0.001 PHE A 26 TYR 0.008 0.001 TYR D 175 ARG 0.002 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 1.321 Fit side-chains outliers start: 52 outliers final: 13 residues processed: 303 average time/residue: 0.2331 time to fit residues: 104.5644 Evaluate side-chains 270 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1125 time to fit residues: 4.6037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.0070 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13616 Z= 0.188 Angle : 0.613 8.223 18384 Z= 0.287 Chirality : 0.040 0.130 2140 Planarity : 0.004 0.057 2224 Dihedral : 15.005 133.060 2288 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.05 % Allowed : 27.92 % Favored : 70.03 % 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 (0.23), residues: 1576 helix: 0.89 (0.17), residues: 1016 sheet: 0.65 (0.60), residues: 88 loop : -0.25 (0.32), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.002 0.001 HIS B 149 PHE 0.017 0.001 PHE A 26 TYR 0.011 0.001 TYR A 270 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 1.490 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 283 average time/residue: 0.2473 time to fit residues: 103.4920 Evaluate side-chains 274 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1175 time to fit residues: 5.6000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13616 Z= 0.288 Angle : 0.661 7.811 18384 Z= 0.314 Chirality : 0.042 0.130 2140 Planarity : 0.004 0.053 2224 Dihedral : 14.566 133.248 2288 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.05 % Allowed : 28.29 % Favored : 69.66 % 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: 0.55 (0.22), residues: 1576 helix: 0.78 (0.17), residues: 1016 sheet: 0.73 (0.61), residues: 88 loop : -0.42 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 264 HIS 0.005 0.001 HIS A 149 PHE 0.013 0.001 PHE A 26 TYR 0.017 0.001 TYR C 175 ARG 0.003 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 1.399 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 268 average time/residue: 0.2497 time to fit residues: 98.4856 Evaluate side-chains 257 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1209 time to fit residues: 4.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13616 Z= 0.191 Angle : 0.650 10.066 18384 Z= 0.300 Chirality : 0.041 0.131 2140 Planarity : 0.004 0.051 2224 Dihedral : 13.549 132.074 2288 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.61 % Allowed : 28.14 % Favored : 70.25 % 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 (0.23), residues: 1576 helix: 0.83 (0.17), residues: 1012 sheet: 0.69 (0.62), residues: 88 loop : -0.41 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 264 HIS 0.002 0.001 HIS C 149 PHE 0.012 0.001 PHE A 26 TYR 0.010 0.001 TYR A 270 ARG 0.002 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 1.587 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 260 average time/residue: 0.2405 time to fit residues: 92.1431 Evaluate side-chains 257 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1146 time to fit residues: 4.8678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0970 chunk 17 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.0370 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 0.0970 chunk 91 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.1252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13616 Z= 0.154 Angle : 0.639 8.990 18384 Z= 0.295 Chirality : 0.040 0.134 2140 Planarity : 0.004 0.048 2224 Dihedral : 12.499 130.829 2288 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.66 % Allowed : 28.58 % Favored : 70.76 % 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: 0.83 (0.23), residues: 1576 helix: 1.01 (0.17), residues: 1012 sheet: 0.89 (0.63), residues: 88 loop : -0.33 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 264 HIS 0.001 0.000 HIS A 316 PHE 0.010 0.001 PHE D 26 TYR 0.007 0.001 TYR A 270 ARG 0.002 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 1.492 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 264 average time/residue: 0.2400 time to fit residues: 93.5040 Evaluate side-chains 252 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1194 time to fit residues: 3.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.0470 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13616 Z= 0.214 Angle : 0.653 8.217 18384 Z= 0.304 Chirality : 0.041 0.130 2140 Planarity : 0.004 0.051 2224 Dihedral : 12.570 131.595 2288 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.17 % Allowed : 28.80 % Favored : 70.03 % 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: 0.78 (0.23), residues: 1576 helix: 0.96 (0.17), residues: 1012 sheet: 0.87 (0.63), residues: 88 loop : -0.32 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 264 HIS 0.003 0.001 HIS D 149 PHE 0.006 0.001 PHE A 26 TYR 0.012 0.001 TYR B 175 ARG 0.002 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 250 time to evaluate : 1.411 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 255 average time/residue: 0.2316 time to fit residues: 88.1457 Evaluate side-chains 252 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1194 time to fit residues: 3.6419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13616 Z= 0.199 Angle : 0.650 8.499 18384 Z= 0.302 Chirality : 0.041 0.129 2140 Planarity : 0.004 0.052 2224 Dihedral : 12.301 130.909 2288 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.22 % Allowed : 29.09 % Favored : 70.69 % 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: 0.81 (0.23), residues: 1576 helix: 0.99 (0.17), residues: 1012 sheet: 0.95 (0.64), residues: 88 loop : -0.35 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 264 HIS 0.002 0.001 HIS C 149 PHE 0.008 0.001 PHE A 26 TYR 0.009 0.001 TYR B 175 ARG 0.002 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 1.446 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.2313 time to fit residues: 87.2367 Evaluate side-chains 247 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13616 Z= 0.194 Angle : 0.652 8.454 18384 Z= 0.302 Chirality : 0.041 0.129 2140 Planarity : 0.004 0.053 2224 Dihedral : 12.131 130.784 2288 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.29 % Allowed : 29.75 % Favored : 69.96 % 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: 0.83 (0.23), residues: 1576 helix: 1.01 (0.17), residues: 1012 sheet: 0.92 (0.64), residues: 88 loop : -0.34 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 264 HIS 0.002 0.001 HIS A 149 PHE 0.008 0.001 PHE A 26 TYR 0.010 0.001 TYR D 245 ARG 0.001 0.000 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 1.513 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 254 average time/residue: 0.2469 time to fit residues: 93.1937 Evaluate side-chains 252 residues out of total 1368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 249 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1335 time to fit residues: 2.9787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 123 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 108 optimal weight: 10.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.216954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.171075 restraints weight = 14407.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.157209 restraints weight = 17501.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.155832 restraints weight = 17662.443| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13616 Z= 0.172 Angle : 0.646 8.738 18384 Z= 0.299 Chirality : 0.041 0.130 2140 Planarity : 0.004 0.052 2224 Dihedral : 11.799 130.451 2288 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.29 % Allowed : 30.12 % Favored : 69.59 % 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: 0.87 (0.23), residues: 1576 helix: 1.03 (0.17), residues: 1012 sheet: 1.03 (0.64), residues: 88 loop : -0.33 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 264 HIS 0.001 0.000 HIS A 149 PHE 0.008 0.001 PHE A 26 TYR 0.017 0.001 TYR D 245 ARG 0.001 0.000 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.40 seconds wall clock time: 49 minutes 13.50 seconds (2953.50 seconds total)