Starting phenix.real_space_refine on Thu Mar 21 22:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbq_13299/03_2024/7pbq_13299_neut_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 46 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3150 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 31323 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.46, per 1000 atoms: 0.43 Number of scatterers: 31323 At special positions: 0 Unit cell: (125.35, 139.52, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 46 15.00 Mg 4 11.99 O 3150 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.75 Conformation dependent library (CDL) restraints added in 3.3 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 18 sheets defined 50.2% alpha, 10.9% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 16.57 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.532A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.829A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.893A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.330A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.841A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.544A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.658A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.681A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.589A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.571A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.439A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.838A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.501A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.575A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.671A pdb=" N ASP B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.527A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.625A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.882A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.582A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.807A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.511A pdb=" N GLU C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.785A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.532A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.613A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.606A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.201A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.809A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 233 Processing helix chain 'D' and resid 241 through 250 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'E' and resid 32 through 48 removed outlier: 3.649A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 91 through 99 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.510A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 No H-bonds generated for 'chain 'E' and resid 166 through 169' Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 205 through 211 Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.510A pdb=" N LYS E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.601A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 91 through 100 removed outlier: 3.527A pdb=" N ALA F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 117 through 129 removed outlier: 4.280A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.934A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 203 through 212 removed outlier: 3.646A pdb=" N ARG F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 233 Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.649A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 201 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 Processing sheet with id= B, first strand: chain 'A' and resid 131 through 137 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= D, first strand: chain 'B' and resid 174 through 177 Processing sheet with id= E, first strand: chain 'B' and resid 131 through 136 Processing sheet with id= F, first strand: chain 'B' and resid 308 through 311 Processing sheet with id= G, first strand: chain 'C' and resid 174 through 177 removed outlier: 3.545A pdb=" N ALA C 157 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 131 through 136 Processing sheet with id= I, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= K, first strand: chain 'D' and resid 131 through 136 Processing sheet with id= L, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= M, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= N, first strand: chain 'E' and resid 131 through 136 Processing sheet with id= O, first strand: chain 'E' and resid 308 through 311 Processing sheet with id= P, first strand: chain 'F' and resid 174 through 177 Processing sheet with id= Q, first strand: chain 'F' and resid 131 through 136 Processing sheet with id= R, first strand: chain 'F' and resid 308 through 310 649 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 26.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15439 1.06 - 1.28: 2655 1.28 - 1.50: 6784 1.50 - 1.72: 6587 1.72 - 1.95: 198 Bond restraints: 31663 Sorted by residual: bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 31658 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.90: 818 106.90 - 114.31: 38736 114.31 - 121.73: 12320 121.73 - 129.14: 5373 129.14 - 136.56: 67 Bond angle restraints: 57314 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.72 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.53 106.35 4.18 1.32e+00 5.74e-01 1.00e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 117.45 -9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" C4' DA U 2 " pdb=" O4' DA U 2 " pdb=" C1' DA U 2 " ideal model delta sigma weight residual 109.70 105.06 4.64 1.50e+00 4.44e-01 9.56e+00 angle pdb=" N LEU D 251 " pdb=" CA LEU D 251 " pdb=" C LEU D 251 " ideal model delta sigma weight residual 110.28 105.78 4.50 1.48e+00 4.57e-01 9.24e+00 ... (remaining 57309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.66: 14117 32.66 - 65.32: 546 65.32 - 97.98: 21 97.98 - 130.64: 2 130.64 - 163.30: 4 Dihedral angle restraints: 14690 sinusoidal: 8421 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 100.63 -160.63 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 80.68 -148.41 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 14687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2261 0.078 - 0.156: 234 0.156 - 0.234: 0 0.234 - 0.312: 0 0.312 - 0.390: 1 Chirality restraints: 2496 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 2493 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.392 9.50e-02 1.11e+02 1.39e-01 7.05e+01 pdb=" NE ARG E 160 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.100 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.203 9.50e-02 1.11e+02 8.38e-02 5.92e+01 pdb=" NE ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.090 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.055 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 169 " -0.166 9.50e-02 1.11e+02 6.78e-02 3.80e+01 pdb=" NE ARG C 169 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 169 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 169 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG C 169 " -0.029 2.00e-02 2.50e+03 pdb="HH11 ARG C 169 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 169 " -0.075 2.00e-02 2.50e+03 pdb="HH21 ARG C 169 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 169 " 0.030 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 671 2.13 - 2.75: 55244 2.75 - 3.36: 82612 3.36 - 3.98: 105700 3.98 - 4.60: 171882 Nonbonded interactions: 416109 Sorted by model distance: nonbonded pdb="HH22 ARG F 214 " pdb=" OD2 ASP F 262 " model vdw 1.510 1.850 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.568 1.850 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLU A 299 " pdb="HH11 ARG A 315 " model vdw 1.578 1.850 nonbonded pdb=" O ALA E 138 " pdb=" HG1 THR E 141 " model vdw 1.601 1.850 ... (remaining 416104 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 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.450 Extract box with map and model: 10.760 Check model and map are aligned: 0.470 Set scattering table: 0.230 Process input model: 109.880 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16224 Z= 0.268 Angle : 0.718 10.281 22098 Z= 0.416 Chirality : 0.044 0.390 2496 Planarity : 0.010 0.134 2739 Dihedral : 14.855 163.296 6278 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.19 % Allowed : 1.19 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.62 (0.18), residues: 1902 helix: -0.85 (0.14), residues: 1004 sheet: 0.63 (0.29), residues: 318 loop : 0.25 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS F 54 PHE 0.023 0.003 PHE A 25 TYR 0.027 0.004 TYR D 327 ARG 0.025 0.003 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 479 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8548 (m-40) cc_final: 0.8196 (m-40) REVERT: B 110 ASP cc_start: 0.7843 (t0) cc_final: 0.7637 (t0) REVERT: B 325 MET cc_start: 0.8563 (mmm) cc_final: 0.8118 (mmp) REVERT: C 125 SER cc_start: 0.8513 (m) cc_final: 0.8224 (p) REVERT: C 178 MET cc_start: 0.9154 (mmt) cc_final: 0.8641 (mmt) REVERT: C 199 MET cc_start: 0.7646 (mmp) cc_final: 0.7390 (mmt) REVERT: C 297 MET cc_start: 0.9060 (ttt) cc_final: 0.8833 (ttm) REVERT: D 58 PHE cc_start: 0.7770 (m-80) cc_final: 0.7378 (m-80) REVERT: D 250 MET cc_start: 0.8433 (ttp) cc_final: 0.8207 (ttp) REVERT: D 269 MET cc_start: 0.8636 (mtp) cc_final: 0.8402 (mtm) REVERT: D 313 THR cc_start: 0.8252 (m) cc_final: 0.8024 (m) REVERT: E 105 ASP cc_start: 0.7654 (m-30) cc_final: 0.7406 (m-30) REVERT: E 111 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 163 MET cc_start: 0.7378 (mmp) cc_final: 0.7046 (mmp) REVERT: E 165 SER cc_start: 0.7385 (t) cc_final: 0.7132 (m) REVERT: E 204 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 243 ILE cc_start: 0.8848 (mm) cc_final: 0.8611 (mt) REVERT: F 117 MET cc_start: 0.7773 (tpt) cc_final: 0.7530 (tpt) REVERT: F 284 SER cc_start: 0.8901 (m) cc_final: 0.8552 (t) REVERT: F 292 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7673 (mm-30) REVERT: F 296 ASP cc_start: 0.7881 (m-30) cc_final: 0.7680 (m-30) outliers start: 3 outliers final: 1 residues processed: 481 average time/residue: 0.8197 time to fit residues: 528.6188 Evaluate side-chains 328 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 166 ASN C 99 ASN F 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16224 Z= 0.222 Angle : 0.601 6.066 22098 Z= 0.326 Chirality : 0.040 0.159 2496 Planarity : 0.005 0.074 2739 Dihedral : 14.898 171.623 2554 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.00 % Allowed : 7.99 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1902 helix: 0.46 (0.16), residues: 1011 sheet: 0.85 (0.29), residues: 317 loop : 0.37 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 146 PHE 0.010 0.001 PHE E 58 TYR 0.016 0.001 TYR E 230 ARG 0.005 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 323 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8588 (m-40) cc_final: 0.8070 (m110) REVERT: B 99 ASN cc_start: 0.7882 (t0) cc_final: 0.7525 (t0) REVERT: B 325 MET cc_start: 0.8561 (mmm) cc_final: 0.8347 (mmp) REVERT: C 178 MET cc_start: 0.9179 (mmt) cc_final: 0.8657 (mmt) REVERT: C 199 MET cc_start: 0.7703 (mmp) cc_final: 0.7424 (mmt) REVERT: C 297 MET cc_start: 0.9091 (ttt) cc_final: 0.8881 (ttm) REVERT: D 58 PHE cc_start: 0.7846 (m-80) cc_final: 0.7531 (m-80) REVERT: D 169 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7639 (ttm-80) REVERT: E 165 SER cc_start: 0.7346 (t) cc_final: 0.6902 (p) REVERT: E 243 ILE cc_start: 0.8679 (mm) cc_final: 0.8449 (mt) REVERT: F 117 MET cc_start: 0.7454 (tpt) cc_final: 0.7045 (tpt) REVERT: F 284 SER cc_start: 0.8890 (m) cc_final: 0.8485 (t) REVERT: F 292 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7689 (mm-30) REVERT: F 325 MET cc_start: 0.7252 (mmt) cc_final: 0.7043 (mmt) outliers start: 16 outliers final: 12 residues processed: 331 average time/residue: 0.7525 time to fit residues: 346.9458 Evaluate side-chains 314 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 302 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain F residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16224 Z= 0.191 Angle : 0.529 5.815 22098 Z= 0.281 Chirality : 0.039 0.140 2496 Planarity : 0.004 0.068 2739 Dihedral : 14.858 179.369 2554 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.19 % Allowed : 7.86 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.10 (0.19), residues: 1902 helix: 0.99 (0.17), residues: 1014 sheet: 0.85 (0.29), residues: 314 loop : 0.45 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.010 0.001 PHE C 25 TYR 0.018 0.001 TYR E 230 ARG 0.009 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 321 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8776 (mmm) cc_final: 0.8545 (mmm) REVERT: A 99 ASN cc_start: 0.8537 (m-40) cc_final: 0.8073 (m110) REVERT: B 117 MET cc_start: 0.6905 (tpp) cc_final: 0.6598 (tpp) REVERT: B 325 MET cc_start: 0.8610 (mmm) cc_final: 0.8387 (mmp) REVERT: C 178 MET cc_start: 0.9168 (mmt) cc_final: 0.8662 (mmt) REVERT: C 297 MET cc_start: 0.9065 (ttt) cc_final: 0.8849 (ttm) REVERT: D 24 TYR cc_start: 0.7157 (m-80) cc_final: 0.6819 (m-80) REVERT: D 58 PHE cc_start: 0.7879 (m-80) cc_final: 0.7591 (m-80) REVERT: D 110 ASP cc_start: 0.7634 (t0) cc_final: 0.7376 (t0) REVERT: D 169 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7608 (ttm-80) REVERT: E 105 ASP cc_start: 0.7587 (m-30) cc_final: 0.7378 (m-30) REVERT: E 165 SER cc_start: 0.7409 (t) cc_final: 0.6978 (p) REVERT: E 243 ILE cc_start: 0.8729 (mm) cc_final: 0.8481 (mt) REVERT: E 252 ASP cc_start: 0.8380 (t70) cc_final: 0.8179 (t0) REVERT: F 267 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8056 (tpp80) REVERT: F 325 MET cc_start: 0.7159 (mmt) cc_final: 0.6849 (mmt) REVERT: G 162 GLU cc_start: 0.6130 (mt-10) cc_final: 0.5730 (mt-10) outliers start: 19 outliers final: 11 residues processed: 331 average time/residue: 0.7853 time to fit residues: 364.6302 Evaluate side-chains 316 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 284 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16224 Z= 0.221 Angle : 0.527 5.889 22098 Z= 0.278 Chirality : 0.039 0.138 2496 Planarity : 0.004 0.051 2739 Dihedral : 14.798 174.378 2552 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.25 % Allowed : 9.30 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.19 (0.19), residues: 1902 helix: 1.18 (0.17), residues: 1013 sheet: 0.77 (0.29), residues: 314 loop : 0.32 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 54 PHE 0.008 0.001 PHE E 58 TYR 0.013 0.001 TYR D 131 ARG 0.008 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 317 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8729 (mmm) cc_final: 0.8489 (mmm) REVERT: A 99 ASN cc_start: 0.8457 (m-40) cc_final: 0.8204 (m110) REVERT: B 117 MET cc_start: 0.6997 (tpp) cc_final: 0.6687 (tpp) REVERT: B 325 MET cc_start: 0.8627 (mmm) cc_final: 0.8418 (mmp) REVERT: C 178 MET cc_start: 0.9162 (mmt) cc_final: 0.8606 (mmt) REVERT: D 110 ASP cc_start: 0.7601 (t0) cc_final: 0.7338 (t0) REVERT: E 105 ASP cc_start: 0.7566 (m-30) cc_final: 0.7344 (m-30) REVERT: E 165 SER cc_start: 0.7451 (t) cc_final: 0.7058 (p) REVERT: E 243 ILE cc_start: 0.8767 (mm) cc_final: 0.8512 (mt) REVERT: E 252 ASP cc_start: 0.8423 (t70) cc_final: 0.8157 (t0) REVERT: E 327 TYR cc_start: 0.7568 (m-80) cc_final: 0.7325 (m-80) REVERT: F 267 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8166 (tpp80) REVERT: F 325 MET cc_start: 0.7189 (mmt) cc_final: 0.6936 (mmt) REVERT: G 162 GLU cc_start: 0.6108 (mt-10) cc_final: 0.5761 (mt-10) outliers start: 20 outliers final: 18 residues processed: 325 average time/residue: 0.7468 time to fit residues: 337.2277 Evaluate side-chains 324 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16224 Z= 0.240 Angle : 0.527 5.888 22098 Z= 0.279 Chirality : 0.039 0.137 2496 Planarity : 0.005 0.045 2739 Dihedral : 14.783 170.831 2552 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.56 % Allowed : 10.23 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.21 (0.19), residues: 1902 helix: 1.23 (0.17), residues: 1013 sheet: 0.75 (0.29), residues: 316 loop : 0.27 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE E 58 TYR 0.015 0.001 TYR A 298 ARG 0.005 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 320 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8732 (mmm) cc_final: 0.8503 (mmm) REVERT: A 99 ASN cc_start: 0.8472 (m-40) cc_final: 0.8218 (m110) REVERT: B 117 MET cc_start: 0.6992 (tpp) cc_final: 0.6704 (tpp) REVERT: B 325 MET cc_start: 0.8657 (mmm) cc_final: 0.8446 (mmp) REVERT: C 178 MET cc_start: 0.9150 (mmt) cc_final: 0.8524 (mmt) REVERT: D 24 TYR cc_start: 0.7485 (m-80) cc_final: 0.7083 (m-80) REVERT: D 110 ASP cc_start: 0.7694 (t0) cc_final: 0.7457 (t0) REVERT: E 105 ASP cc_start: 0.7611 (m-30) cc_final: 0.7375 (m-30) REVERT: E 148 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: E 165 SER cc_start: 0.7486 (t) cc_final: 0.7077 (p) REVERT: E 243 ILE cc_start: 0.8778 (mm) cc_final: 0.8510 (mt) REVERT: E 327 TYR cc_start: 0.7562 (m-80) cc_final: 0.7291 (m-80) REVERT: F 325 MET cc_start: 0.7238 (mmt) cc_final: 0.6994 (mmt) REVERT: G 162 GLU cc_start: 0.6136 (mt-10) cc_final: 0.5792 (mt-10) outliers start: 25 outliers final: 21 residues processed: 331 average time/residue: 0.7646 time to fit residues: 350.5788 Evaluate side-chains 334 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN C 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 16224 Z= 0.234 Angle : 0.532 5.891 22098 Z= 0.280 Chirality : 0.039 0.131 2496 Planarity : 0.005 0.068 2739 Dihedral : 14.761 169.747 2552 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.68 % Allowed : 10.61 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.20 (0.19), residues: 1902 helix: 1.28 (0.17), residues: 1011 sheet: 0.71 (0.29), residues: 316 loop : 0.18 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE E 58 TYR 0.014 0.001 TYR A 298 ARG 0.010 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 317 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8724 (mmm) cc_final: 0.8505 (mmm) REVERT: A 99 ASN cc_start: 0.8488 (m-40) cc_final: 0.8227 (m110) REVERT: B 117 MET cc_start: 0.7037 (tpp) cc_final: 0.6749 (tpp) REVERT: B 325 MET cc_start: 0.8641 (mmm) cc_final: 0.8434 (mmp) REVERT: C 178 MET cc_start: 0.9137 (mmt) cc_final: 0.8523 (mmt) REVERT: D 110 ASP cc_start: 0.7690 (t0) cc_final: 0.7451 (t0) REVERT: E 105 ASP cc_start: 0.7617 (m-30) cc_final: 0.7366 (m-30) REVERT: E 148 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: E 165 SER cc_start: 0.7516 (t) cc_final: 0.7108 (p) REVERT: E 243 ILE cc_start: 0.8700 (mm) cc_final: 0.8448 (mt) REVERT: E 295 GLU cc_start: 0.7877 (tt0) cc_final: 0.7477 (mt-10) REVERT: E 327 TYR cc_start: 0.7566 (m-80) cc_final: 0.7333 (m-80) REVERT: G 162 GLU cc_start: 0.6145 (mt-10) cc_final: 0.5799 (mt-10) outliers start: 27 outliers final: 22 residues processed: 328 average time/residue: 0.7556 time to fit residues: 341.2777 Evaluate side-chains 336 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16224 Z= 0.286 Angle : 0.553 7.484 22098 Z= 0.292 Chirality : 0.040 0.133 2496 Planarity : 0.005 0.070 2739 Dihedral : 14.812 168.045 2552 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.75 % Allowed : 11.29 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.08 (0.19), residues: 1902 helix: 1.20 (0.17), residues: 1015 sheet: 0.67 (0.29), residues: 316 loop : 0.08 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 54 PHE 0.009 0.001 PHE D 25 TYR 0.014 0.001 TYR A 298 ARG 0.008 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 312 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8701 (mmm) cc_final: 0.8479 (mmm) REVERT: A 99 ASN cc_start: 0.8520 (m-40) cc_final: 0.8220 (m110) REVERT: B 117 MET cc_start: 0.7083 (tpp) cc_final: 0.6798 (tpp) REVERT: B 325 MET cc_start: 0.8648 (mmm) cc_final: 0.8444 (mmp) REVERT: C 178 MET cc_start: 0.9136 (mmt) cc_final: 0.8459 (mmt) REVERT: E 105 ASP cc_start: 0.7662 (m-30) cc_final: 0.7389 (m-30) REVERT: E 148 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: E 165 SER cc_start: 0.7548 (t) cc_final: 0.7143 (p) REVERT: E 243 ILE cc_start: 0.8722 (mm) cc_final: 0.8462 (mt) REVERT: E 295 GLU cc_start: 0.7861 (tt0) cc_final: 0.7565 (mt-10) REVERT: E 327 TYR cc_start: 0.7571 (m-80) cc_final: 0.7354 (m-80) REVERT: G 162 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5806 (mt-10) outliers start: 28 outliers final: 25 residues processed: 325 average time/residue: 0.7723 time to fit residues: 345.9973 Evaluate side-chains 333 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16224 Z= 0.214 Angle : 0.534 9.309 22098 Z= 0.279 Chirality : 0.039 0.132 2496 Planarity : 0.005 0.055 2739 Dihedral : 14.758 168.464 2552 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.56 % Allowed : 11.73 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.18 (0.20), residues: 1902 helix: 1.31 (0.17), residues: 1015 sheet: 0.64 (0.29), residues: 316 loop : 0.10 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 255 PHE 0.008 0.001 PHE D 25 TYR 0.014 0.001 TYR A 298 ARG 0.010 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8678 (mmm) cc_final: 0.8461 (mmm) REVERT: A 99 ASN cc_start: 0.8515 (m-40) cc_final: 0.8238 (m110) REVERT: B 117 MET cc_start: 0.7086 (tpp) cc_final: 0.6802 (tpp) REVERT: B 325 MET cc_start: 0.8672 (mmm) cc_final: 0.8461 (mmp) REVERT: C 178 MET cc_start: 0.9123 (mmt) cc_final: 0.8440 (mmt) REVERT: E 105 ASP cc_start: 0.7667 (m-30) cc_final: 0.7377 (m-30) REVERT: E 148 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: E 165 SER cc_start: 0.7505 (t) cc_final: 0.7100 (p) REVERT: E 241 ASP cc_start: 0.7442 (p0) cc_final: 0.7066 (t0) REVERT: E 243 ILE cc_start: 0.8713 (mm) cc_final: 0.8448 (mt) REVERT: E 295 GLU cc_start: 0.7846 (tt0) cc_final: 0.7560 (mt-10) REVERT: G 162 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5747 (mt-10) outliers start: 25 outliers final: 23 residues processed: 320 average time/residue: 0.7532 time to fit residues: 331.7616 Evaluate side-chains 336 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16224 Z= 0.191 Angle : 0.523 5.990 22098 Z= 0.272 Chirality : 0.039 0.132 2496 Planarity : 0.005 0.086 2739 Dihedral : 14.676 168.050 2552 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.50 % Allowed : 12.10 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.32 (0.20), residues: 1902 helix: 1.42 (0.17), residues: 1015 sheet: 0.66 (0.29), residues: 316 loop : 0.19 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.010 0.001 PHE D 58 TYR 0.012 0.001 TYR D 131 ARG 0.012 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 316 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8697 (mmm) cc_final: 0.8485 (mmm) REVERT: A 99 ASN cc_start: 0.8501 (m-40) cc_final: 0.8218 (m110) REVERT: B 117 MET cc_start: 0.7065 (tpp) cc_final: 0.6788 (tpp) REVERT: B 325 MET cc_start: 0.8658 (mmm) cc_final: 0.8436 (mmp) REVERT: C 178 MET cc_start: 0.9090 (mmt) cc_final: 0.8392 (mmt) REVERT: C 199 MET cc_start: 0.7604 (mmt) cc_final: 0.7256 (mmt) REVERT: E 105 ASP cc_start: 0.7673 (m-30) cc_final: 0.7366 (m-30) REVERT: E 148 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: E 165 SER cc_start: 0.7486 (t) cc_final: 0.7074 (p) REVERT: E 243 ILE cc_start: 0.8697 (mm) cc_final: 0.8426 (mt) REVERT: E 295 GLU cc_start: 0.7830 (tt0) cc_final: 0.7574 (mt-10) REVERT: G 162 GLU cc_start: 0.6089 (mt-10) cc_final: 0.5759 (mt-10) outliers start: 24 outliers final: 22 residues processed: 324 average time/residue: 0.8145 time to fit residues: 367.2376 Evaluate side-chains 333 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 310 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16224 Z= 0.229 Angle : 0.539 11.308 22098 Z= 0.280 Chirality : 0.039 0.134 2496 Planarity : 0.005 0.072 2739 Dihedral : 14.663 167.085 2552 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.29 (0.20), residues: 1902 helix: 1.40 (0.17), residues: 1014 sheet: 0.66 (0.29), residues: 316 loop : 0.17 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 54 PHE 0.010 0.001 PHE D 25 TYR 0.012 0.001 TYR D 131 ARG 0.014 0.000 ARG F 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 316 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8678 (mmm) cc_final: 0.8463 (mmm) REVERT: A 99 ASN cc_start: 0.8513 (m-40) cc_final: 0.8223 (m110) REVERT: B 117 MET cc_start: 0.7081 (tpp) cc_final: 0.6810 (tpp) REVERT: B 325 MET cc_start: 0.8647 (mmm) cc_final: 0.8424 (mmp) REVERT: C 178 MET cc_start: 0.9090 (mmt) cc_final: 0.8399 (mmt) REVERT: E 102 GLU cc_start: 0.7114 (tt0) cc_final: 0.6783 (tt0) REVERT: E 105 ASP cc_start: 0.7683 (m-30) cc_final: 0.7371 (m-30) REVERT: E 148 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: E 165 SER cc_start: 0.7492 (t) cc_final: 0.7081 (p) REVERT: E 241 ASP cc_start: 0.7440 (p0) cc_final: 0.7074 (t0) REVERT: E 295 GLU cc_start: 0.7831 (tt0) cc_final: 0.7628 (mt-10) REVERT: G 162 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5828 (mt-10) outliers start: 27 outliers final: 23 residues processed: 325 average time/residue: 0.8038 time to fit residues: 362.2468 Evaluate side-chains 336 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.103404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.078350 restraints weight = 73884.534| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.24 r_work: 0.2750 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16224 Z= 0.223 Angle : 0.530 5.881 22098 Z= 0.277 Chirality : 0.039 0.134 2496 Planarity : 0.005 0.085 2739 Dihedral : 14.630 166.697 2552 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.56 % Allowed : 12.54 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.30 (0.20), residues: 1902 helix: 1.41 (0.17), residues: 1014 sheet: 0.66 (0.29), residues: 316 loop : 0.18 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 255 PHE 0.009 0.001 PHE A 58 TYR 0.012 0.001 TYR D 131 ARG 0.011 0.000 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8502.75 seconds wall clock time: 151 minutes 2.59 seconds (9062.59 seconds total)