Starting phenix.real_space_refine on Wed Feb 21 11:58:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbr_13300/02_2024/7pbr_13300_neut_trim_updated.pdb" } resolution = 3.0 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 100 5.16 5 C 9682 2.51 5 N 2619 2.21 5 O 3076 1.98 5 H 15077 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30604 Number of models: 1 Model: "" Number of chains: 14 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: "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: 12.72, per 1000 atoms: 0.42 Number of scatterers: 30604 At special positions: 0 Unit cell: (124.26, 138.43, 103.55, 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 100 16.00 P 46 15.00 Mg 4 11.99 O 3076 8.00 N 2619 7.00 C 9682 6.00 H 15077 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: 23.91 Conformation dependent library (CDL) restraints added in 3.4 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 18 sheets defined 49.9% alpha, 11.2% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 15.71 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.617A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.656A 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: 3.549A 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: 4.571A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (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: 3.911A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.751A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.531A 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 251 removed outlier: 3.738A 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 removed outlier: 3.530A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.574A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) 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: 3.505A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.705A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.511A 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: 4.415A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (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: 3.743A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.558A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.969A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 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: 3.673A pdb=" N ILE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.638A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.642A 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 128 removed outlier: 4.160A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.859A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.523A pdb=" N GLU C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (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: 3.879A 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 286 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 Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.674A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) 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 removed outlier: 3.513A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) 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: 4.086A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.935A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.706A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 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 47 removed outlier: 3.509A 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 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' 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: 3.556A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.216A 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 removed outlier: 3.662A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 212 removed outlier: 3.617A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 234 removed outlier: 4.122A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.766A 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 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 291 through 296 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: 3.604A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.735A 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: 4.626A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (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 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.191A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.561A pdb=" N GLU F 188 " --> pdb=" O PRO F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 217 through 233 Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.638A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.528A 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 304 Processing helix chain 'F' and resid 319 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.507A pdb=" N ALA A 157 " --> pdb=" O ILE A 109 " (cutoff:3.500A) 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 removed outlier: 3.528A pdb=" N ALA B 157 " --> pdb=" O ILE B 109 " (cutoff:3.500A) 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: 3.582A 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 removed outlier: 3.695A pdb=" N ASP D 110 " --> pdb=" O THR D 83 " (cutoff:3.500A) 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 310 617 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.09 Time building geometry restraints manager: 24.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15077 1.05 - 1.28: 2588 1.28 - 1.50: 6574 1.50 - 1.72: 6507 1.72 - 1.95: 196 Bond restraints: 30942 Sorted by residual: bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 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 2.52e+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 2.51e+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 F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 30937 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.55: 716 106.55 - 114.05: 37487 114.05 - 121.54: 12132 121.54 - 129.03: 5598 129.03 - 136.53: 73 Bond angle restraints: 56006 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 120.00 109.82 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 117.02 -9.02 3.00e+00 1.11e-01 9.03e+00 angle pdb=" N MET D 250 " pdb=" CA MET D 250 " pdb=" C MET D 250 " ideal model delta sigma weight residual 111.14 107.89 3.25 1.08e+00 8.57e-01 9.03e+00 angle pdb=" N GLU A 140 " pdb=" CA GLU A 140 " pdb=" C GLU A 140 " ideal model delta sigma weight residual 111.40 107.87 3.53 1.22e+00 6.72e-01 8.39e+00 angle pdb=" C2' ADP F 600 " pdb=" C3' ADP F 600 " pdb=" C4' ADP F 600 " ideal model delta sigma weight residual 111.00 102.57 8.43 3.00e+00 1.11e-01 7.90e+00 ... (remaining 56001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 13730 31.16 - 62.32: 591 62.32 - 93.48: 27 93.48 - 124.63: 0 124.63 - 155.79: 6 Dihedral angle restraints: 14354 sinusoidal: 8231 harmonic: 6123 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 95.79 -155.79 1 2.00e+01 2.50e-03 4.59e+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 89.63 -149.63 1 2.00e+01 2.50e-03 4.47e+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 62.78 -130.51 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 14351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2178 0.075 - 0.149: 258 0.149 - 0.224: 1 0.224 - 0.298: 0 0.298 - 0.373: 1 Chirality restraints: 2438 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 -2.72 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA PRO D 300 " pdb=" N PRO D 300 " pdb=" C PRO D 300 " pdb=" CB PRO D 300 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.43e-01 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 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2435 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.069 9.50e-02 1.11e+02 6.18e-02 7.46e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.111 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.036 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.008 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 211 " -0.364 9.50e-02 1.11e+02 1.30e-01 6.43e+01 pdb=" NE ARG E 211 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 211 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 211 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG E 211 " 0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 211 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 211 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG E 211 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG E 211 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.173 9.50e-02 1.11e+02 7.71e-02 6.25e+01 pdb=" NE ARG C 192 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.093 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.095 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 677 2.12 - 2.74: 53414 2.74 - 3.36: 81136 3.36 - 3.98: 104216 3.98 - 4.60: 168402 Nonbonded interactions: 407845 Sorted by model distance: nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.505 1.850 nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.556 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.559 1.850 nonbonded pdb=" OE2 GLU A 299 " pdb="HH21 ARG A 310 " model vdw 1.574 1.850 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.579 1.850 ... (remaining 407840 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: 2.230 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: 0.480 Extract box with map and model: 11.090 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 105.610 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.090 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.038 15865 Z= 0.265 Angle : 0.715 10.184 21613 Z= 0.413 Chirality : 0.045 0.373 2438 Planarity : 0.009 0.119 2674 Dihedral : 15.019 155.793 6140 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.13 % Allowed : 1.15 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.67 (0.18), residues: 1856 helix: -1.03 (0.15), residues: 970 sheet: 0.70 (0.29), residues: 322 loop : 0.42 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 177 PHE 0.024 0.003 PHE A 25 TYR 0.022 0.005 TYR D 124 ARG 0.026 0.003 ARG E 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 454 time to evaluate : 2.155 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: symmetry clash REVERT: A 81 LYS cc_start: 0.8032 (mttp) cc_final: 0.7828 (mttt) REVERT: A 287 ILE cc_start: 0.8447 (pt) cc_final: 0.8134 (pt) REVERT: A 325 MET cc_start: 0.8599 (mmm) cc_final: 0.8266 (mmm) REVERT: C 325 MET cc_start: 0.9002 (mmm) cc_final: 0.8747 (mmm) REVERT: D 232 GLN cc_start: 0.8699 (pt0) cc_final: 0.8464 (pt0) REVERT: E 23 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7405 (mm110) REVERT: E 230 TYR cc_start: 0.7457 (t80) cc_final: 0.7236 (t80) REVERT: E 260 TYR cc_start: 0.7616 (t80) cc_final: 0.7393 (t80) REVERT: E 310 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7205 (ptp-110) REVERT: F 37 GLN cc_start: 0.8640 (mt0) cc_final: 0.8438 (mt0) REVERT: F 225 LYS cc_start: 0.8747 (mttt) cc_final: 0.8541 (mtmm) REVERT: F 297 MET cc_start: 0.8282 (tpp) cc_final: 0.7785 (tmm) outliers start: 2 outliers final: 2 residues processed: 455 average time/residue: 3.5233 time to fit residues: 1730.3147 Evaluate side-chains 312 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 310 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain C residue 79 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.0270 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 286 ASN E 79 ASN E 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15865 Z= 0.226 Angle : 0.627 6.166 21613 Z= 0.336 Chirality : 0.041 0.145 2438 Planarity : 0.005 0.049 2674 Dihedral : 15.082 156.334 2503 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.17 % Allowed : 15.57 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.19), residues: 1856 helix: 0.44 (0.17), residues: 964 sheet: 1.14 (0.29), residues: 298 loop : 0.39 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 146 PHE 0.009 0.001 PHE B 25 TYR 0.012 0.001 TYR C 124 ARG 0.006 0.001 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 330 time to evaluate : 2.647 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: A 83 THR cc_start: 0.9138 (t) cc_final: 0.8863 (m) REVERT: A 143 ARG cc_start: 0.7512 (ptp90) cc_final: 0.7312 (pmm150) REVERT: B 81 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8149 (mmmm) REVERT: C 325 MET cc_start: 0.9004 (mmm) cc_final: 0.8728 (mmm) REVERT: D 188 GLU cc_start: 0.7559 (mp0) cc_final: 0.7232 (mp0) REVERT: D 232 GLN cc_start: 0.8791 (pt0) cc_final: 0.8516 (pt0) REVERT: E 23 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7414 (mm110) REVERT: E 111 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7472 (mt-10) REVERT: F 272 MET cc_start: 0.8068 (ttp) cc_final: 0.7857 (ttp) REVERT: F 295 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7589 (mt-10) REVERT: F 298 TYR cc_start: 0.8755 (m-80) cc_final: 0.8220 (m-80) outliers start: 34 outliers final: 12 residues processed: 343 average time/residue: 3.3312 time to fit residues: 1238.9519 Evaluate side-chains 315 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 250 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 136 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 286 ASN D 177 HIS D 286 ASN E 79 ASN F 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15865 Z= 0.212 Angle : 0.565 7.152 21613 Z= 0.296 Chirality : 0.040 0.165 2438 Planarity : 0.004 0.042 2674 Dihedral : 15.020 159.598 2501 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.23 % Allowed : 17.23 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.13 (0.19), residues: 1856 helix: 0.97 (0.17), residues: 963 sheet: 0.83 (0.29), residues: 314 loop : 0.58 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 177 PHE 0.009 0.001 PHE E 307 TYR 0.008 0.001 TYR A 260 ARG 0.004 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 306 time to evaluate : 2.454 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: A 33 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8212 (mtmm) REVERT: A 83 THR cc_start: 0.9142 (t) cc_final: 0.8877 (m) REVERT: A 260 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6748 (p90) REVERT: B 89 GLU cc_start: 0.7571 (tp30) cc_final: 0.7366 (tp30) REVERT: B 245 ASP cc_start: 0.7101 (p0) cc_final: 0.6830 (p0) REVERT: C 166 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: C 325 MET cc_start: 0.9003 (mmm) cc_final: 0.8689 (mmm) REVERT: E 250 MET cc_start: 0.8410 (tmm) cc_final: 0.7931 (ttt) REVERT: F 272 MET cc_start: 0.7994 (ttp) cc_final: 0.7743 (ttp) REVERT: F 297 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7582 (tmm) REVERT: F 309 MET cc_start: 0.7386 (tpt) cc_final: 0.7010 (tpt) outliers start: 35 outliers final: 14 residues processed: 321 average time/residue: 3.2473 time to fit residues: 1134.2671 Evaluate side-chains 312 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 294 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 260 TYR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15865 Z= 0.256 Angle : 0.569 6.549 21613 Z= 0.299 Chirality : 0.041 0.193 2438 Planarity : 0.004 0.043 2674 Dihedral : 15.072 163.522 2501 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.36 % Allowed : 18.38 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1856 helix: 1.11 (0.17), residues: 963 sheet: 0.75 (0.29), residues: 310 loop : 0.51 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 177 PHE 0.008 0.001 PHE C 108 TYR 0.008 0.001 TYR E 329 ARG 0.005 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 291 time to evaluate : 2.512 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 83 THR cc_start: 0.9161 (t) cc_final: 0.8920 (m) REVERT: A 260 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6768 (p90) REVERT: B 89 GLU cc_start: 0.7593 (tp30) cc_final: 0.7358 (tp30) REVERT: B 111 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: C 325 MET cc_start: 0.9007 (mmm) cc_final: 0.8653 (mmm) REVERT: E 250 MET cc_start: 0.8416 (tmm) cc_final: 0.7961 (ttt) REVERT: F 68 MET cc_start: 0.8564 (tpp) cc_final: 0.8282 (tpt) REVERT: F 297 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: F 309 MET cc_start: 0.7403 (tpt) cc_final: 0.7067 (tpt) outliers start: 37 outliers final: 14 residues processed: 312 average time/residue: 3.4355 time to fit residues: 1163.6093 Evaluate side-chains 305 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 288 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 92 optimal weight: 0.0270 chunk 162 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15865 Z= 0.189 Angle : 0.551 7.838 21613 Z= 0.284 Chirality : 0.039 0.151 2438 Planarity : 0.004 0.044 2674 Dihedral : 14.999 162.325 2499 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.17 % Allowed : 18.89 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1856 helix: 1.28 (0.17), residues: 963 sheet: 0.72 (0.29), residues: 310 loop : 0.55 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 177 PHE 0.007 0.001 PHE C 108 TYR 0.012 0.001 TYR D 124 ARG 0.005 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 295 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: A 83 THR cc_start: 0.9131 (t) cc_final: 0.8919 (m) REVERT: A 260 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6701 (p90) REVERT: B 89 GLU cc_start: 0.7672 (tp30) cc_final: 0.7439 (tp30) REVERT: B 111 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: C 166 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: C 234 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7862 (mmt) REVERT: C 325 MET cc_start: 0.8993 (mmm) cc_final: 0.8638 (mmm) REVERT: D 188 GLU cc_start: 0.7442 (mp0) cc_final: 0.7218 (mp0) REVERT: E 81 LYS cc_start: 0.7857 (mppt) cc_final: 0.7158 (mptt) REVERT: E 250 MET cc_start: 0.8419 (tmm) cc_final: 0.7975 (ttt) REVERT: E 292 GLU cc_start: 0.7245 (mp0) cc_final: 0.6995 (mp0) REVERT: F 68 MET cc_start: 0.8542 (tpp) cc_final: 0.8278 (tpt) REVERT: F 309 MET cc_start: 0.7398 (tpt) cc_final: 0.7071 (tpt) outliers start: 34 outliers final: 17 residues processed: 312 average time/residue: 3.4435 time to fit residues: 1165.1568 Evaluate side-chains 306 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 284 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 260 TYR Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 250 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15865 Z= 0.207 Angle : 0.549 8.206 21613 Z= 0.284 Chirality : 0.039 0.129 2438 Planarity : 0.004 0.049 2674 Dihedral : 14.971 162.461 2499 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.30 % Allowed : 19.14 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.38 (0.20), residues: 1856 helix: 1.36 (0.17), residues: 962 sheet: 0.67 (0.29), residues: 310 loop : 0.52 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 177 PHE 0.008 0.001 PHE C 108 TYR 0.015 0.001 TYR E 301 ARG 0.006 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 2.349 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 33 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: A 260 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6720 (p90) REVERT: B 89 GLU cc_start: 0.7683 (tp30) cc_final: 0.7432 (tp30) REVERT: B 111 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 166 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7939 (m-40) REVERT: C 234 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7847 (mmt) REVERT: C 325 MET cc_start: 0.9009 (mmm) cc_final: 0.8699 (mmm) REVERT: D 252 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7274 (t0) REVERT: E 250 MET cc_start: 0.8415 (tmm) cc_final: 0.7935 (ttt) REVERT: F 68 MET cc_start: 0.8549 (tpp) cc_final: 0.8243 (tpt) REVERT: F 297 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: F 309 MET cc_start: 0.7406 (tpt) cc_final: 0.7084 (tpt) outliers start: 36 outliers final: 17 residues processed: 312 average time/residue: 3.4677 time to fit residues: 1175.0640 Evaluate side-chains 316 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 292 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15865 Z= 0.241 Angle : 0.561 7.048 21613 Z= 0.290 Chirality : 0.040 0.133 2438 Planarity : 0.005 0.051 2674 Dihedral : 14.983 164.006 2499 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.30 % Allowed : 19.59 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.33 (0.20), residues: 1856 helix: 1.35 (0.17), residues: 963 sheet: 0.64 (0.29), residues: 310 loop : 0.42 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 177 PHE 0.008 0.001 PHE C 108 TYR 0.018 0.001 TYR D 124 ARG 0.006 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 292 time to evaluate : 2.564 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 33 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8210 (mtmm) REVERT: A 260 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6752 (p90) REVERT: B 89 GLU cc_start: 0.7683 (tp30) cc_final: 0.7445 (tp30) REVERT: B 111 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 166 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7967 (m-40) REVERT: C 272 MET cc_start: 0.7592 (mtp) cc_final: 0.7382 (mtm) REVERT: C 325 MET cc_start: 0.9017 (mmm) cc_final: 0.8694 (mmm) REVERT: D 120 GLU cc_start: 0.7724 (tt0) cc_final: 0.7321 (tm-30) REVERT: D 188 GLU cc_start: 0.7467 (mp0) cc_final: 0.7244 (mp0) REVERT: D 252 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7293 (t0) REVERT: E 250 MET cc_start: 0.8410 (tmm) cc_final: 0.7946 (ttt) REVERT: E 263 GLN cc_start: 0.7988 (mt0) cc_final: 0.7787 (mt0) REVERT: E 305 LYS cc_start: 0.8087 (mppt) cc_final: 0.7704 (mmtp) REVERT: F 68 MET cc_start: 0.8548 (tpp) cc_final: 0.8256 (tpt) REVERT: F 188 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7499 (tp30) REVERT: F 297 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: F 309 MET cc_start: 0.7397 (tpt) cc_final: 0.7098 (tpt) outliers start: 36 outliers final: 16 residues processed: 312 average time/residue: 3.4787 time to fit residues: 1176.9136 Evaluate side-chains 303 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 281 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15865 Z= 0.225 Angle : 0.568 9.324 21613 Z= 0.291 Chirality : 0.040 0.133 2438 Planarity : 0.005 0.059 2674 Dihedral : 14.965 164.498 2499 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.17 % Allowed : 20.23 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1856 helix: 1.36 (0.17), residues: 968 sheet: 0.66 (0.28), residues: 308 loop : 0.36 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 177 PHE 0.007 0.001 PHE C 108 TYR 0.017 0.001 TYR E 301 ARG 0.008 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 286 time to evaluate : 2.429 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: A 33 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8216 (mtmm) REVERT: A 260 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6762 (p90) REVERT: B 89 GLU cc_start: 0.7706 (tp30) cc_final: 0.7452 (tp30) REVERT: B 111 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 166 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7990 (m-40) REVERT: C 272 MET cc_start: 0.7684 (mtp) cc_final: 0.7464 (mtp) REVERT: C 325 MET cc_start: 0.9036 (mmm) cc_final: 0.8702 (mmm) REVERT: D 188 GLU cc_start: 0.7488 (mp0) cc_final: 0.7237 (mp0) REVERT: D 252 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7196 (t0) REVERT: E 250 MET cc_start: 0.8411 (tmm) cc_final: 0.7941 (ttt) REVERT: E 263 GLN cc_start: 0.7953 (mt0) cc_final: 0.7749 (mt0) REVERT: E 305 LYS cc_start: 0.8097 (mppt) cc_final: 0.7728 (mmtp) REVERT: F 68 MET cc_start: 0.8541 (tpp) cc_final: 0.8255 (tpt) REVERT: F 178 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8541 (mtp) REVERT: F 188 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7523 (tp30) REVERT: F 297 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: F 309 MET cc_start: 0.7402 (tpt) cc_final: 0.7102 (tpt) outliers start: 34 outliers final: 18 residues processed: 305 average time/residue: 3.4198 time to fit residues: 1129.3279 Evaluate side-chains 314 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15865 Z= 0.230 Angle : 0.566 6.772 21613 Z= 0.290 Chirality : 0.040 0.143 2438 Planarity : 0.005 0.061 2674 Dihedral : 14.965 165.649 2499 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.85 % Allowed : 20.36 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1856 helix: 1.39 (0.17), residues: 967 sheet: 0.65 (0.28), residues: 308 loop : 0.28 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 177 PHE 0.007 0.001 PHE A 172 TYR 0.016 0.001 TYR D 124 ARG 0.010 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 290 time to evaluate : 2.482 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: A 260 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6777 (p90) REVERT: B 89 GLU cc_start: 0.7731 (tp30) cc_final: 0.7433 (tp30) REVERT: B 111 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 166 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.8001 (m-40) REVERT: C 325 MET cc_start: 0.9023 (mmm) cc_final: 0.8679 (mmm) REVERT: D 252 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7215 (t0) REVERT: E 250 MET cc_start: 0.8390 (tmm) cc_final: 0.7941 (ttt) REVERT: E 263 GLN cc_start: 0.7967 (mt0) cc_final: 0.7750 (mt0) REVERT: E 305 LYS cc_start: 0.8086 (mppt) cc_final: 0.7740 (mmtp) REVERT: F 68 MET cc_start: 0.8546 (tpp) cc_final: 0.8264 (tpt) REVERT: F 178 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: F 188 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7523 (tp30) REVERT: F 297 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7637 (tmm) REVERT: F 309 MET cc_start: 0.7455 (tpt) cc_final: 0.7146 (tpt) outliers start: 29 outliers final: 17 residues processed: 306 average time/residue: 3.5070 time to fit residues: 1166.2914 Evaluate side-chains 304 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 281 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 286 ASN D 177 HIS E 79 ASN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15865 Z= 0.202 Angle : 0.570 10.737 21613 Z= 0.290 Chirality : 0.039 0.145 2438 Planarity : 0.005 0.074 2674 Dihedral : 14.930 164.515 2499 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.91 % Allowed : 20.87 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.20), residues: 1856 helix: 1.48 (0.18), residues: 967 sheet: 0.66 (0.28), residues: 308 loop : 0.32 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 177 PHE 0.006 0.001 PHE B 58 TYR 0.030 0.001 TYR D 124 ARG 0.009 0.000 ARG D 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 290 time to evaluate : 2.380 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: A 33 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: A 260 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6777 (p90) REVERT: B 89 GLU cc_start: 0.7708 (tp30) cc_final: 0.7411 (tp30) REVERT: B 111 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 166 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7987 (m-40) REVERT: C 325 MET cc_start: 0.9004 (mmm) cc_final: 0.8655 (mmm) REVERT: E 250 MET cc_start: 0.8373 (tmm) cc_final: 0.7934 (ttt) REVERT: E 263 GLN cc_start: 0.7968 (mt0) cc_final: 0.7758 (mt0) REVERT: F 68 MET cc_start: 0.8534 (tpp) cc_final: 0.8250 (tpt) REVERT: F 178 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8498 (mtp) REVERT: F 188 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7530 (tp30) REVERT: F 297 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7635 (tmm) REVERT: F 309 MET cc_start: 0.7511 (tpt) cc_final: 0.7230 (tpt) outliers start: 30 outliers final: 16 residues processed: 305 average time/residue: 3.4436 time to fit residues: 1137.4768 Evaluate side-chains 308 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 286 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS E 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.075831 restraints weight = 69732.983| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.29 r_work: 0.2788 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15865 Z= 0.244 Angle : 0.584 9.534 21613 Z= 0.298 Chirality : 0.040 0.145 2438 Planarity : 0.005 0.070 2674 Dihedral : 14.959 165.911 2499 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.47 % Allowed : 21.57 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1856 helix: 1.40 (0.17), residues: 966 sheet: 0.63 (0.28), residues: 308 loop : 0.24 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 177 PHE 0.007 0.001 PHE A 172 TYR 0.020 0.001 TYR D 124 ARG 0.008 0.001 ARG D 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16814.13 seconds wall clock time: 292 minutes 44.66 seconds (17564.66 seconds total)