Starting phenix.real_space_refine on Sat Mar 16 00:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cjt_7483/03_2024/6cjt_7483_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8748 2.51 5 N 2128 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 403": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13208 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "B" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "C" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "D" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 7.06, per 1000 atoms: 0.53 Number of scatterers: 13208 At special positions: 0 Unit cell: (106.322, 106.322, 120.571, 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 2296 8.00 N 2128 7.00 C 8748 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: 5.15 Conformation dependent library (CDL) restraints added in 2.3 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 56.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 Proline residue: A 31 - end of helix removed outlier: 3.732A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 62 removed outlier: 4.446A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 102 through 125 removed outlier: 4.261A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.864A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.950A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 223 removed outlier: 3.835A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.506A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.617A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'B' and resid 13 through 35 Proline residue: B 31 - end of helix removed outlier: 3.732A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 62 removed outlier: 4.446A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 102 through 125 removed outlier: 4.261A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.864A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.950A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 223 removed outlier: 3.835A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.506A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.617A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'C' and resid 13 through 35 Proline residue: C 31 - end of helix removed outlier: 3.732A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.446A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 102 through 125 removed outlier: 4.261A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.864A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.950A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 3.835A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.506A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.617A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'D' and resid 13 through 35 Proline residue: D 31 - end of helix removed outlier: 3.732A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 62 removed outlier: 4.446A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 102 through 125 removed outlier: 4.261A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.864A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.950A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 223 removed outlier: 3.835A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.506A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 293 through 296 No H-bonds generated for 'chain 'D' and resid 293 through 296' Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.617A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 405 through 410 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= B, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.516A pdb=" N VAL A 346 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= D, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.516A pdb=" N VAL B 346 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'C' and resid 380 through 383 removed outlier: 3.516A pdb=" N VAL C 346 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= H, first strand: chain 'D' and resid 380 through 383 removed outlier: 3.516A pdb=" N VAL D 346 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1680 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: 3.62 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3220 1.33 - 1.45: 2404 1.45 - 1.57: 7788 1.57 - 1.69: 24 1.69 - 1.81: 48 Bond restraints: 13484 Sorted by residual: bond pdb=" C2' PCG C 500 " pdb=" C3' PCG C 500 " ideal model delta sigma weight residual 1.200 1.501 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2' PCG D 500 " pdb=" C3' PCG D 500 " ideal model delta sigma weight residual 1.200 1.501 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2' PCG A 500 " pdb=" C3' PCG A 500 " ideal model delta sigma weight residual 1.200 1.501 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C2' PCG B 500 " pdb=" C3' PCG B 500 " ideal model delta sigma weight residual 1.200 1.501 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C1' PCG D 500 " pdb=" N9 PCG D 500 " ideal model delta sigma weight residual 1.216 1.493 -0.277 2.00e-02 2.50e+03 1.92e+02 ... (remaining 13479 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.22: 468 106.22 - 113.23: 7468 113.23 - 120.24: 5380 120.24 - 127.25: 4760 127.25 - 134.26: 160 Bond angle restraints: 18236 Sorted by residual: angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 ... (remaining 18231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 8016 35.00 - 70.00: 160 70.00 - 105.01: 32 105.01 - 140.01: 24 140.01 - 175.01: 8 Dihedral angle restraints: 8240 sinusoidal: 3580 harmonic: 4660 Sorted by residual: dihedral pdb=" CA LEU D 276 " pdb=" C LEU D 276 " pdb=" N LYS D 277 " pdb=" CA LYS D 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU C 276 " pdb=" C LEU C 276 " pdb=" N LYS C 277 " pdb=" CA LYS C 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 8237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1888 0.101 - 0.202: 216 0.202 - 0.303: 8 0.303 - 0.404: 8 0.404 - 0.505: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" C3' PCG A 500 " pdb=" C2' PCG A 500 " pdb=" C4' PCG A 500 " pdb=" O3' PCG A 500 " both_signs ideal model delta sigma weight residual False -2.10 -2.61 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C3' PCG B 500 " pdb=" C2' PCG B 500 " pdb=" C4' PCG B 500 " pdb=" O3' PCG B 500 " both_signs ideal model delta sigma weight residual False -2.10 -2.61 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C3' PCG D 500 " pdb=" C2' PCG D 500 " pdb=" C4' PCG D 500 " pdb=" O3' PCG D 500 " both_signs ideal model delta sigma weight residual False -2.10 -2.61 0.50 2.00e-01 2.50e+01 6.37e+00 ... (remaining 2121 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU A 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU D 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU D 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 94 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.019 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3416 2.80 - 3.33: 11668 3.33 - 3.85: 21092 3.85 - 4.38: 23032 4.38 - 4.90: 41232 Nonbonded interactions: 100440 Sorted by model distance: nonbonded pdb=" OD2 ASP B 312 " pdb=" OH TYR B 404 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP C 312 " pdb=" OH TYR C 404 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP D 312 " pdb=" OH TYR D 404 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP A 312 " pdb=" OH TYR A 404 " model vdw 2.280 2.440 nonbonded pdb=" O12 PGW A 501 " pdb=" OAE PGW A 501 " model vdw 2.295 2.440 ... (remaining 100435 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 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'B' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'C' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'D' and (resid 10 through 412 or resid 502 or (resid 504 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 505 and (name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C30)) or (resid 506 and (name C15 or name C16 or name C17 or \ name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.270 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.980 Find NCS groups from input model: 0.970 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.015 0.301 13484 Z= 1.029 Angle : 1.426 9.945 18236 Z= 0.673 Chirality : 0.070 0.505 2124 Planarity : 0.008 0.058 2200 Dihedral : 17.587 175.011 5232 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % 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: -3.58 (0.18), residues: 1568 helix: -2.14 (0.14), residues: 924 sheet: -2.51 (0.39), residues: 84 loop : -2.47 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 264 HIS 0.005 0.001 HIS D 149 PHE 0.012 0.002 PHE B 36 TYR 0.030 0.004 TYR D 211 ARG 0.007 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7501 (tm) cc_final: 0.7279 (mt) REVERT: A 158 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9091 (pp) REVERT: A 229 LYS cc_start: 0.8979 (tmtp) cc_final: 0.8746 (ttmt) REVERT: A 272 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 388 ASP cc_start: 0.8234 (m-30) cc_final: 0.7800 (t0) REVERT: B 77 LEU cc_start: 0.7492 (tm) cc_final: 0.7291 (mt) REVERT: B 229 LYS cc_start: 0.8974 (tmtp) cc_final: 0.8755 (ttmt) REVERT: B 272 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 388 ASP cc_start: 0.8204 (m-30) cc_final: 0.7820 (t0) REVERT: C 77 LEU cc_start: 0.7528 (tm) cc_final: 0.7309 (mt) REVERT: C 272 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 388 ASP cc_start: 0.8222 (m-30) cc_final: 0.7970 (t0) REVERT: D 77 LEU cc_start: 0.7519 (tm) cc_final: 0.7295 (mt) REVERT: D 158 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9066 (pp) REVERT: D 229 LYS cc_start: 0.8981 (tmtp) cc_final: 0.8738 (ttmt) REVERT: D 272 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 388 ASP cc_start: 0.8216 (m-30) cc_final: 0.7815 (t0) outliers start: 8 outliers final: 0 residues processed: 240 average time/residue: 0.2928 time to fit residues: 96.3954 Evaluate side-chains 97 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13484 Z= 0.188 Angle : 0.696 7.587 18236 Z= 0.325 Chirality : 0.043 0.224 2124 Planarity : 0.005 0.047 2200 Dihedral : 19.300 168.103 2232 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.31 % Allowed : 9.93 % Favored : 86.76 % 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: -1.35 (0.21), residues: 1568 helix: -0.29 (0.17), residues: 924 sheet: -1.60 (0.47), residues: 92 loop : -1.65 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 264 HIS 0.001 0.001 HIS C 149 PHE 0.008 0.001 PHE B 96 TYR 0.014 0.001 TYR B 128 ARG 0.002 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 1.550 Fit side-chains REVERT: A 77 LEU cc_start: 0.7513 (tm) cc_final: 0.7310 (mt) REVERT: A 171 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 369 MET cc_start: 0.7992 (mmm) cc_final: 0.7755 (mmt) REVERT: B 171 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8743 (tp) REVERT: B 369 MET cc_start: 0.8065 (mmm) cc_final: 0.7820 (mmt) REVERT: C 77 LEU cc_start: 0.7528 (tm) cc_final: 0.7316 (mt) REVERT: C 171 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (tp) REVERT: C 229 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8598 (ttpt) REVERT: C 369 MET cc_start: 0.8060 (mmm) cc_final: 0.7813 (mmt) REVERT: D 77 LEU cc_start: 0.7525 (tm) cc_final: 0.7310 (mt) REVERT: D 171 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8750 (tp) REVERT: D 369 MET cc_start: 0.8023 (mmm) cc_final: 0.7787 (mmt) outliers start: 45 outliers final: 7 residues processed: 162 average time/residue: 0.2584 time to fit residues: 60.0890 Evaluate side-chains 96 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13484 Z= 0.256 Angle : 0.699 11.070 18236 Z= 0.319 Chirality : 0.044 0.214 2124 Planarity : 0.004 0.028 2200 Dihedral : 17.483 153.954 2228 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 12.57 % Favored : 84.19 % 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: -0.20 (0.23), residues: 1568 helix: 0.66 (0.18), residues: 912 sheet: -1.01 (0.52), residues: 92 loop : -1.20 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 264 HIS 0.003 0.001 HIS C 149 PHE 0.008 0.001 PHE D 96 TYR 0.021 0.001 TYR B 11 ARG 0.004 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 time to evaluate : 1.513 Fit side-chains REVERT: A 60 LEU cc_start: 0.8404 (tp) cc_final: 0.8134 (tt) REVERT: A 77 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7084 (mt) REVERT: A 171 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 369 MET cc_start: 0.8098 (mmm) cc_final: 0.7811 (mmt) REVERT: B 60 LEU cc_start: 0.8380 (tp) cc_final: 0.8092 (tt) REVERT: B 171 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8752 (tp) REVERT: B 369 MET cc_start: 0.8093 (mmm) cc_final: 0.7814 (mmt) REVERT: C 60 LEU cc_start: 0.8391 (tp) cc_final: 0.8106 (tt) REVERT: C 77 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7103 (mt) REVERT: C 171 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 369 MET cc_start: 0.8100 (mmm) cc_final: 0.7806 (mmt) REVERT: D 60 LEU cc_start: 0.8409 (tp) cc_final: 0.8145 (tt) REVERT: D 77 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7213 (mt) REVERT: D 171 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8762 (tp) REVERT: D 369 MET cc_start: 0.8102 (mmm) cc_final: 0.7800 (mmt) outliers start: 44 outliers final: 21 residues processed: 139 average time/residue: 0.2412 time to fit residues: 50.1018 Evaluate side-chains 105 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 0.0000 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13484 Z= 0.143 Angle : 0.637 11.257 18236 Z= 0.284 Chirality : 0.041 0.189 2124 Planarity : 0.003 0.024 2200 Dihedral : 14.499 110.243 2228 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.60 % Allowed : 13.38 % Favored : 83.01 % 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: 0.41 (0.23), residues: 1568 helix: 1.16 (0.18), residues: 912 sheet: -0.78 (0.53), residues: 92 loop : -0.96 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 264 HIS 0.001 0.000 HIS A 232 PHE 0.005 0.001 PHE D 242 TYR 0.011 0.001 TYR B 128 ARG 0.003 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 97 time to evaluate : 1.499 Fit side-chains REVERT: A 60 LEU cc_start: 0.8395 (tp) cc_final: 0.8152 (tt) REVERT: A 77 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6963 (mt) REVERT: A 171 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 221 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8899 (tt) REVERT: A 369 MET cc_start: 0.8001 (mmm) cc_final: 0.7735 (mmt) REVERT: B 60 LEU cc_start: 0.8380 (tp) cc_final: 0.8112 (tt) REVERT: B 171 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8757 (tp) REVERT: B 221 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 369 MET cc_start: 0.8088 (mmm) cc_final: 0.7810 (mmt) REVERT: C 60 LEU cc_start: 0.8411 (tp) cc_final: 0.8145 (tt) REVERT: C 77 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7174 (mt) REVERT: C 171 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (tp) REVERT: C 221 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8890 (tt) REVERT: C 369 MET cc_start: 0.8074 (mmm) cc_final: 0.7790 (mmt) REVERT: D 47 ASP cc_start: 0.7450 (m-30) cc_final: 0.6853 (m-30) REVERT: D 60 LEU cc_start: 0.8404 (tp) cc_final: 0.8159 (tt) REVERT: D 77 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7194 (mt) REVERT: D 171 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8739 (tp) REVERT: D 221 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8904 (tt) REVERT: D 369 MET cc_start: 0.7991 (mmm) cc_final: 0.7724 (mmt) outliers start: 49 outliers final: 22 residues processed: 141 average time/residue: 0.2331 time to fit residues: 49.3179 Evaluate side-chains 109 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13484 Z= 0.206 Angle : 0.666 10.733 18236 Z= 0.296 Chirality : 0.043 0.183 2124 Planarity : 0.003 0.024 2200 Dihedral : 13.099 95.149 2228 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.24 % Allowed : 14.71 % Favored : 82.06 % 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: 0.72 (0.23), residues: 1568 helix: 1.47 (0.18), residues: 912 sheet: -0.88 (0.53), residues: 84 loop : -0.89 (0.29), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS C 232 PHE 0.005 0.001 PHE D 366 TYR 0.021 0.001 TYR B 11 ARG 0.002 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 84 time to evaluate : 1.433 Fit side-chains REVERT: A 60 LEU cc_start: 0.8455 (tp) cc_final: 0.8223 (tt) REVERT: A 77 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7124 (mt) REVERT: A 171 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 221 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 60 LEU cc_start: 0.8408 (tp) cc_final: 0.8157 (tt) REVERT: B 171 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8719 (tp) REVERT: B 221 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 369 MET cc_start: 0.8108 (mmm) cc_final: 0.7892 (mmm) REVERT: C 60 LEU cc_start: 0.8415 (tp) cc_final: 0.8153 (tt) REVERT: C 77 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7106 (mt) REVERT: C 171 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (tp) REVERT: C 221 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8937 (tt) REVERT: D 60 LEU cc_start: 0.8414 (tp) cc_final: 0.8178 (tt) REVERT: D 77 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7153 (mt) REVERT: D 171 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8733 (tp) REVERT: D 221 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8954 (tt) outliers start: 44 outliers final: 29 residues processed: 123 average time/residue: 0.2280 time to fit residues: 42.4273 Evaluate side-chains 117 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 77 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13484 Z= 0.152 Angle : 0.630 11.034 18236 Z= 0.277 Chirality : 0.041 0.183 2124 Planarity : 0.003 0.023 2200 Dihedral : 12.256 92.594 2228 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.31 % Allowed : 15.44 % Favored : 81.25 % 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: 0.93 (0.23), residues: 1568 helix: 1.60 (0.18), residues: 924 sheet: -0.87 (0.54), residues: 84 loop : -0.78 (0.30), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.002 0.000 HIS A 232 PHE 0.005 0.001 PHE D 366 TYR 0.008 0.001 TYR D 128 ARG 0.003 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 85 time to evaluate : 1.547 Fit side-chains REVERT: A 60 LEU cc_start: 0.8410 (tp) cc_final: 0.8170 (tt) REVERT: A 77 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7151 (mt) REVERT: A 221 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8985 (tt) REVERT: B 60 LEU cc_start: 0.8398 (tp) cc_final: 0.8138 (tt) REVERT: B 221 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8993 (tt) REVERT: C 60 LEU cc_start: 0.8399 (tp) cc_final: 0.8138 (tt) REVERT: C 77 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7166 (mt) REVERT: C 221 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8989 (tt) REVERT: D 60 LEU cc_start: 0.8428 (tp) cc_final: 0.8171 (tt) REVERT: D 77 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7179 (mt) REVERT: D 221 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8986 (tt) outliers start: 45 outliers final: 28 residues processed: 123 average time/residue: 0.2259 time to fit residues: 42.3432 Evaluate side-chains 112 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13484 Z= 0.206 Angle : 0.688 12.443 18236 Z= 0.296 Chirality : 0.042 0.180 2124 Planarity : 0.003 0.024 2200 Dihedral : 12.069 97.577 2228 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.53 % Allowed : 15.07 % Favored : 81.40 % 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: 1.09 (0.23), residues: 1568 helix: 1.69 (0.18), residues: 928 sheet: -0.86 (0.54), residues: 84 loop : -0.65 (0.30), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.002 0.001 HIS D 149 PHE 0.005 0.001 PHE C 309 TYR 0.028 0.001 TYR B 11 ARG 0.002 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 77 time to evaluate : 1.376 Fit side-chains REVERT: A 60 LEU cc_start: 0.8447 (tp) cc_final: 0.8236 (tt) REVERT: A 77 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7162 (mt) REVERT: A 221 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8991 (tt) REVERT: B 60 LEU cc_start: 0.8454 (tp) cc_final: 0.8211 (tt) REVERT: B 171 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8684 (tp) REVERT: B 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8990 (tt) REVERT: C 60 LEU cc_start: 0.8457 (tp) cc_final: 0.8204 (tt) REVERT: C 77 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7140 (mt) REVERT: C 221 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8988 (tt) REVERT: D 60 LEU cc_start: 0.8491 (tp) cc_final: 0.8272 (tt) REVERT: D 77 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7155 (mt) REVERT: D 221 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8990 (tt) outliers start: 48 outliers final: 32 residues processed: 120 average time/residue: 0.2312 time to fit residues: 42.4828 Evaluate side-chains 112 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 72 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13484 Z= 0.179 Angle : 0.653 11.165 18236 Z= 0.283 Chirality : 0.042 0.184 2124 Planarity : 0.003 0.024 2200 Dihedral : 11.539 96.412 2228 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.16 % Allowed : 14.85 % Favored : 81.99 % 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: 1.26 (0.23), residues: 1568 helix: 1.83 (0.18), residues: 928 sheet: -0.90 (0.54), residues: 84 loop : -0.56 (0.30), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.002 0.001 HIS D 149 PHE 0.005 0.001 PHE B 366 TYR 0.010 0.001 TYR D 128 ARG 0.002 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 86 time to evaluate : 1.466 Fit side-chains REVERT: A 62 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7767 (mm) REVERT: A 77 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7157 (mt) REVERT: A 221 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8975 (tt) REVERT: B 221 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8971 (tt) REVERT: C 60 LEU cc_start: 0.8469 (tp) cc_final: 0.8222 (tt) REVERT: C 77 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7160 (mt) REVERT: C 221 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8969 (tt) REVERT: D 60 LEU cc_start: 0.8489 (tp) cc_final: 0.8264 (tt) REVERT: D 62 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7944 (mm) REVERT: D 77 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7167 (mt) REVERT: D 221 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8972 (tt) outliers start: 43 outliers final: 30 residues processed: 125 average time/residue: 0.2316 time to fit residues: 44.2936 Evaluate side-chains 116 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 77 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13484 Z= 0.179 Angle : 0.663 10.859 18236 Z= 0.285 Chirality : 0.042 0.184 2124 Planarity : 0.003 0.023 2200 Dihedral : 11.364 96.757 2228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.24 % Allowed : 14.93 % Favored : 81.84 % 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: 1.34 (0.23), residues: 1568 helix: 1.89 (0.18), residues: 928 sheet: -0.95 (0.55), residues: 84 loop : -0.50 (0.30), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 264 HIS 0.002 0.001 HIS B 149 PHE 0.004 0.001 PHE A 366 TYR 0.017 0.001 TYR B 11 ARG 0.002 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 1.427 Fit side-chains REVERT: A 62 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 77 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7070 (mt) REVERT: A 221 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8974 (tt) REVERT: B 171 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 221 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8970 (tt) REVERT: C 60 LEU cc_start: 0.8449 (tp) cc_final: 0.8205 (tt) REVERT: C 77 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7154 (mt) REVERT: C 221 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8994 (tt) REVERT: D 60 LEU cc_start: 0.8468 (tp) cc_final: 0.8242 (tt) REVERT: D 62 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7946 (mm) REVERT: D 77 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7080 (mt) REVERT: D 221 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8997 (tt) outliers start: 44 outliers final: 32 residues processed: 126 average time/residue: 0.1945 time to fit residues: 37.7633 Evaluate side-chains 119 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 77 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS D 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13484 Z= 0.166 Angle : 0.668 16.413 18236 Z= 0.283 Chirality : 0.042 0.195 2124 Planarity : 0.003 0.023 2200 Dihedral : 11.121 95.733 2228 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.09 % Allowed : 15.51 % Favored : 81.40 % 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: 1.40 (0.23), residues: 1568 helix: 1.94 (0.18), residues: 928 sheet: -0.99 (0.56), residues: 84 loop : -0.47 (0.30), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 264 HIS 0.002 0.001 HIS B 232 PHE 0.004 0.001 PHE B 366 TYR 0.009 0.001 TYR D 128 ARG 0.002 0.000 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 87 time to evaluate : 1.526 Fit side-chains REVERT: A 62 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 77 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7104 (mt) REVERT: A 171 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 221 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8987 (tt) REVERT: B 171 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8674 (tp) REVERT: B 221 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8983 (tt) REVERT: C 60 LEU cc_start: 0.8484 (tp) cc_final: 0.8212 (tt) REVERT: C 77 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7122 (mt) REVERT: C 221 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8982 (tt) REVERT: D 60 LEU cc_start: 0.8472 (tp) cc_final: 0.8252 (tt) REVERT: D 62 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8000 (mm) REVERT: D 77 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7109 (mt) REVERT: D 221 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8985 (tt) outliers start: 42 outliers final: 29 residues processed: 125 average time/residue: 0.2193 time to fit residues: 42.1480 Evaluate side-chains 123 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 83 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.117644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088664 restraints weight = 24274.594| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.20 r_work: 0.2947 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13484 Z= 0.135 Angle : 0.642 14.076 18236 Z= 0.272 Chirality : 0.041 0.183 2124 Planarity : 0.003 0.023 2200 Dihedral : 10.665 92.468 2228 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.65 % Allowed : 16.25 % Favored : 81.10 % 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: 1.53 (0.23), residues: 1568 helix: 2.19 (0.18), residues: 904 sheet: -1.05 (0.56), residues: 84 loop : -0.55 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.002 0.001 HIS D 232 PHE 0.004 0.001 PHE B 366 TYR 0.019 0.001 TYR B 11 ARG 0.002 0.000 ARG B 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.01 seconds wall clock time: 42 minutes 39.09 seconds (2559.09 seconds total)