Starting phenix.real_space_refine on Wed Feb 21 22:19:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbn_13296/02_2024/7pbn_13296_neut_trim_updated.pdb" } resolution = 3.2 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 44 5.49 5 Mg 3 5.21 5 S 100 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3218 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32074 Number of models: 1 Model: "" Number of chains: 16 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: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 14.19, per 1000 atoms: 0.44 Number of scatterers: 32074 At special positions: 0 Unit cell: (125.35, 138.43, 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 100 16.00 P 44 15.00 Mg 3 11.99 O 3218 8.00 N 2757 7.00 C 10134 6.00 H 15818 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: 27.85 Conformation dependent library (CDL) restraints added in 3.4 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 17 sheets defined 50.6% alpha, 10.5% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 18.83 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.517A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.760A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (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: 3.660A 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 128 removed outlier: 4.538A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.518A 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: 3.890A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.676A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.661A pdb=" N GLU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.874A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.610A pdb=" N ILE A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.540A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.659A 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 Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.603A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) 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: 4.611A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.563A 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 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.600A pdb=" N GLU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.615A pdb=" N GLU B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.508A pdb=" N TYR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) 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 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 32 through 47 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.770A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.978A 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: 3.984A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (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 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.570A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.558A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 removed outlier: 3.663A pdb=" N ILE C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.749A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.521A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) 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: 3.611A 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 91 through 100 removed outlier: 3.684A 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: 4.438A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.634A 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 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.586A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 4.180A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.631A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (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 272 Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.589A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) 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: 3.621A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.748A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) 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: 4.489A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.985A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.710A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.634A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 removed outlier: 3.551A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) 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 removed outlier: 3.591A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.902A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.520A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) 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: 3.579A 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: 4.731A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.505A 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 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 169 No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.671A 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 Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.874A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.596A 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 helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 201 Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 191 through 198 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.660A pdb=" N GLY A 59 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 131 through 136 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 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: 3.580A 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 'E' and resid 174 through 177 Processing sheet with id= M, first strand: chain 'E' and resid 131 through 136 Processing sheet with id= N, first strand: chain 'E' and resid 308 through 311 Processing sheet with id= O, first strand: chain 'F' and resid 174 through 177 Processing sheet with id= P, first strand: chain 'F' and resid 131 through 136 Processing sheet with id= Q, first strand: chain 'F' and resid 308 through 311 641 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.22 Time building geometry restraints manager: 27.77 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: 15818 1.06 - 1.28: 2721 1.28 - 1.50: 6867 1.50 - 1.72: 6817 1.72 - 1.94: 198 Bond restraints: 32421 Sorted by residual: 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 2.52e+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 2.51e+01 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 2.51e+01 bond pdb=" N ASP H 158 " pdb=" H1 ASP H 158 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+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 2.49e+01 ... (remaining 32416 not shown) Histogram of bond angle deviations from ideal: 98.55 - 106.13: 687 106.13 - 113.72: 38850 113.72 - 121.30: 12893 121.30 - 128.88: 6162 128.88 - 136.47: 92 Bond angle restraints: 58684 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 120.00 110.18 9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.70 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 109.70 105.14 4.56 1.50e+00 4.44e-01 9.24e+00 angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 102.43 8.57 3.00e+00 1.11e-01 8.15e+00 angle pdb=" C1' ADP E 600 " pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " ideal model delta sigma weight residual 111.00 102.44 8.56 3.00e+00 1.11e-01 8.15e+00 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 14411 31.28 - 62.57: 581 62.57 - 93.85: 31 93.85 - 125.14: 2 125.14 - 156.42: 5 Dihedral angle restraints: 15030 sinusoidal: 8597 harmonic: 6433 Sorted by residual: 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 96.42 -156.42 1 2.00e+01 2.50e-03 4.60e+01 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 91.76 -151.76 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 79.17 -139.17 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 15027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2280 0.070 - 0.139: 266 0.139 - 0.209: 5 0.209 - 0.278: 0 0.278 - 0.348: 1 Chirality restraints: 2552 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 -2.69 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 2549 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 218 " 0.037 9.50e-02 1.11e+02 5.02e-02 5.34e+01 pdb=" NE ARG F 218 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG F 218 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG F 218 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 218 " -0.093 2.00e-02 2.50e+03 pdb="HH11 ARG F 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 218 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG F 218 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG F 218 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.100 9.50e-02 1.11e+02 5.50e-02 4.40e+01 pdb=" NE ARG A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.074 2.00e-02 2.50e+03 pdb="HH11 ARG A 192 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 192 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 192 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.039 2.00e-02 2.50e+03 4.82e-02 3.49e+01 pdb=" CD GLN C 31 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.077 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.074 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 724 2.13 - 2.75: 56384 2.75 - 3.36: 84799 3.36 - 3.98: 108181 3.98 - 4.60: 175611 Nonbonded interactions: 425699 Sorted by model distance: nonbonded pdb=" HG1 THR F 311 " pdb=" O GLY F 314 " model vdw 1.509 1.850 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.558 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.580 1.850 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.582 1.850 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.590 1.850 ... (remaining 425694 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)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } 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: 2.500 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: 0.490 Extract box with map and model: 11.010 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 115.530 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.039 16603 Z= 0.249 Angle : 0.727 9.817 22607 Z= 0.410 Chirality : 0.044 0.348 2552 Planarity : 0.010 0.153 2808 Dihedral : 14.915 156.423 6403 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.88 (0.18), residues: 1950 helix: -1.20 (0.14), residues: 1039 sheet: 0.50 (0.29), residues: 304 loop : 0.46 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS B 324 PHE 0.020 0.003 PHE C 25 TYR 0.039 0.005 TYR D 131 ARG 0.027 0.004 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 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: 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 68 MET cc_start: 0.8566 (tpp) cc_final: 0.8357 (tpp) REVERT: A 76 MET cc_start: 0.9093 (mmm) cc_final: 0.8778 (mmt) REVERT: A 105 ASP cc_start: 0.7834 (m-30) cc_final: 0.7607 (m-30) REVERT: A 296 ASP cc_start: 0.7518 (m-30) cc_final: 0.7305 (m-30) REVERT: B 295 GLU cc_start: 0.8089 (tt0) cc_final: 0.7830 (tt0) REVERT: C 90 LYS cc_start: 0.8236 (pttt) cc_final: 0.8033 (pttp) REVERT: C 178 MET cc_start: 0.9169 (mmt) cc_final: 0.7934 (mmt) REVERT: C 291 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7979 (ttm170) REVERT: D 68 MET cc_start: 0.9164 (tpt) cc_final: 0.8559 (tpt) REVERT: D 171 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8070 (mpt90) REVERT: D 309 MET cc_start: 0.8894 (mtp) cc_final: 0.8598 (mtp) REVERT: E 178 MET cc_start: 0.9253 (mmm) cc_final: 0.9023 (mmt) REVERT: E 256 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 272 MET cc_start: 0.8013 (mtt) cc_final: 0.7750 (mtt) REVERT: F 117 MET cc_start: 0.7951 (tpt) cc_final: 0.7527 (tpt) REVERT: F 213 SER cc_start: 0.8588 (t) cc_final: 0.8355 (p) REVERT: G 164 VAL cc_start: 0.8569 (t) cc_final: 0.8252 (p) REVERT: G 180 MET cc_start: 0.6892 (mtp) cc_final: 0.6613 (mtm) REVERT: G 203 LEU cc_start: 0.7626 (tp) cc_final: 0.6586 (tp) REVERT: H 194 LEU cc_start: 0.8917 (mt) cc_final: 0.8670 (mt) outliers start: 1 outliers final: 1 residues processed: 416 average time/residue: 0.8994 time to fit residues: 504.0144 Evaluate side-chains 262 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 2.669 ------------------------------------------------------------------------------- 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: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 99 ASN D 166 ASN D 246 GLN F 255 HIS H 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16603 Z= 0.256 Angle : 0.613 6.357 22607 Z= 0.325 Chirality : 0.041 0.152 2552 Planarity : 0.005 0.042 2808 Dihedral : 14.716 149.177 2590 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.98 % Allowed : 6.15 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.17 (0.19), residues: 1950 helix: -0.00 (0.15), residues: 1055 sheet: 0.63 (0.28), residues: 331 loop : 0.43 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 255 PHE 0.010 0.001 PHE A 58 TYR 0.021 0.001 TYR C 124 ARG 0.006 0.001 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 269 time to evaluate : 2.745 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: 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: 0.9008 (mmm) cc_final: 0.8735 (mmt) REVERT: A 163 MET cc_start: 0.8216 (mmm) cc_final: 0.7894 (mmt) REVERT: A 296 ASP cc_start: 0.7574 (m-30) cc_final: 0.7373 (m-30) REVERT: B 295 GLU cc_start: 0.8112 (tt0) cc_final: 0.7828 (tt0) REVERT: C 325 MET cc_start: 0.9017 (mmp) cc_final: 0.8704 (mmp) REVERT: D 171 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.8154 (mpt90) REVERT: D 309 MET cc_start: 0.8887 (mtp) cc_final: 0.8567 (mtp) REVERT: E 256 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7567 (mm-30) REVERT: E 272 MET cc_start: 0.7989 (mtt) cc_final: 0.7668 (mtt) REVERT: F 213 SER cc_start: 0.8498 (t) cc_final: 0.8207 (p) REVERT: F 295 GLU cc_start: 0.7728 (tt0) cc_final: 0.7229 (tt0) outliers start: 16 outliers final: 14 residues processed: 276 average time/residue: 0.7698 time to fit residues: 301.7524 Evaluate side-chains 271 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.0000 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 143 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN F 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16603 Z= 0.182 Angle : 0.547 8.526 22607 Z= 0.280 Chirality : 0.039 0.154 2552 Planarity : 0.004 0.041 2808 Dihedral : 14.498 141.198 2590 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.85 % Allowed : 7.68 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.75 (0.19), residues: 1950 helix: 0.60 (0.16), residues: 1058 sheet: 0.72 (0.28), residues: 330 loop : 0.49 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 146 PHE 0.007 0.001 PHE A 58 TYR 0.017 0.001 TYR C 124 ARG 0.004 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 264 time to evaluate : 2.440 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8216 (mmm) cc_final: 0.7905 (mmt) REVERT: B 295 GLU cc_start: 0.8079 (tt0) cc_final: 0.7811 (tt0) REVERT: C 325 MET cc_start: 0.8984 (mmp) cc_final: 0.8632 (mmp) REVERT: D 171 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8137 (mpt90) REVERT: D 309 MET cc_start: 0.8873 (mtp) cc_final: 0.8547 (mtp) REVERT: E 256 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7572 (mm-30) REVERT: E 272 MET cc_start: 0.7962 (mtt) cc_final: 0.7648 (mtt) REVERT: F 213 SER cc_start: 0.8524 (t) cc_final: 0.8307 (p) REVERT: F 295 GLU cc_start: 0.7760 (tt0) cc_final: 0.7225 (tt0) REVERT: F 329 TYR cc_start: 0.7952 (t80) cc_final: 0.7434 (t80) REVERT: G 176 GLU cc_start: 0.8257 (tp30) cc_final: 0.8001 (tp30) outliers start: 14 outliers final: 13 residues processed: 271 average time/residue: 0.7407 time to fit residues: 283.0916 Evaluate side-chains 266 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 253 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.0040 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16603 Z= 0.213 Angle : 0.539 7.340 22607 Z= 0.275 Chirality : 0.039 0.157 2552 Planarity : 0.004 0.045 2808 Dihedral : 14.348 136.902 2590 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.58 % Allowed : 7.92 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.94 (0.19), residues: 1950 helix: 0.88 (0.17), residues: 1053 sheet: 0.53 (0.29), residues: 317 loop : 0.50 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 146 PHE 0.008 0.001 PHE B 58 TYR 0.018 0.001 TYR C 124 ARG 0.009 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.235 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 163 MET cc_start: 0.8256 (mmm) cc_final: 0.7927 (mmt) REVERT: B 295 GLU cc_start: 0.8076 (tt0) cc_final: 0.7826 (tt0) REVERT: C 325 MET cc_start: 0.8893 (mmp) cc_final: 0.8524 (mmp) REVERT: D 171 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8115 (mpt90) REVERT: D 309 MET cc_start: 0.8885 (mtp) cc_final: 0.8556 (mtp) REVERT: E 272 MET cc_start: 0.8014 (mtt) cc_final: 0.7545 (mtt) REVERT: F 211 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8237 (ttp-110) REVERT: F 246 GLN cc_start: 0.8712 (mt0) cc_final: 0.8434 (mt0) REVERT: F 295 GLU cc_start: 0.7761 (tt0) cc_final: 0.7085 (tt0) REVERT: F 329 TYR cc_start: 0.7952 (t80) cc_final: 0.7418 (t80) outliers start: 26 outliers final: 21 residues processed: 270 average time/residue: 0.7637 time to fit residues: 291.9372 Evaluate side-chains 270 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain F residue 287 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.0030 chunk 78 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16603 Z= 0.196 Angle : 0.533 6.816 22607 Z= 0.271 Chirality : 0.039 0.151 2552 Planarity : 0.004 0.044 2808 Dihedral : 14.248 136.561 2590 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.34 % Allowed : 8.78 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.04 (0.19), residues: 1950 helix: 1.01 (0.17), residues: 1051 sheet: 0.53 (0.29), residues: 317 loop : 0.48 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 146 PHE 0.007 0.001 PHE B 58 TYR 0.017 0.001 TYR C 124 ARG 0.006 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 2.495 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: symmetry clash REVERT: A 163 MET cc_start: 0.8252 (mmm) cc_final: 0.7932 (mmt) REVERT: B 295 GLU cc_start: 0.8069 (tt0) cc_final: 0.7824 (tt0) REVERT: C 325 MET cc_start: 0.8877 (mmp) cc_final: 0.8485 (mmp) REVERT: D 171 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8062 (mpt90) REVERT: D 309 MET cc_start: 0.8880 (mtp) cc_final: 0.8539 (mtp) REVERT: E 272 MET cc_start: 0.8004 (mtt) cc_final: 0.7540 (mtt) REVERT: F 211 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8239 (ttp-110) REVERT: F 246 GLN cc_start: 0.8704 (mt0) cc_final: 0.8400 (mt0) REVERT: F 295 GLU cc_start: 0.7770 (tt0) cc_final: 0.7104 (tt0) outliers start: 22 outliers final: 18 residues processed: 267 average time/residue: 0.7851 time to fit residues: 299.2804 Evaluate side-chains 269 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 0.2980 chunk 37 optimal weight: 0.0170 chunk 111 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 166 ASN E 23 GLN H 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16603 Z= 0.151 Angle : 0.513 11.373 22607 Z= 0.258 Chirality : 0.038 0.166 2552 Planarity : 0.004 0.047 2808 Dihedral : 14.046 136.844 2590 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.34 % Allowed : 9.14 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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 (0.19), residues: 1950 helix: 1.28 (0.17), residues: 1049 sheet: 0.69 (0.29), residues: 304 loop : 0.52 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 146 PHE 0.006 0.001 PHE B 58 TYR 0.014 0.001 TYR C 124 ARG 0.005 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 263 time to evaluate : 2.382 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8249 (mmm) cc_final: 0.7954 (mmt) REVERT: C 133 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7582 (p0) REVERT: D 171 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7959 (mpt90) REVERT: D 309 MET cc_start: 0.8862 (mtp) cc_final: 0.8505 (mtp) REVERT: E 272 MET cc_start: 0.7989 (mtt) cc_final: 0.7532 (mtt) REVERT: F 211 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8242 (ttp-110) REVERT: F 246 GLN cc_start: 0.8711 (mt0) cc_final: 0.8382 (mt0) REVERT: F 267 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.7996 (ttp-110) REVERT: F 295 GLU cc_start: 0.7773 (tt0) cc_final: 0.7098 (tt0) outliers start: 22 outliers final: 18 residues processed: 274 average time/residue: 0.7360 time to fit residues: 286.7868 Evaluate side-chains 270 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16603 Z= 0.324 Angle : 0.567 6.175 22607 Z= 0.292 Chirality : 0.041 0.168 2552 Planarity : 0.005 0.048 2808 Dihedral : 14.219 140.088 2590 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.58 % Allowed : 9.26 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.94 (0.19), residues: 1950 helix: 1.01 (0.17), residues: 1047 sheet: 0.54 (0.29), residues: 303 loop : 0.22 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 146 PHE 0.009 0.001 PHE B 58 TYR 0.020 0.001 TYR C 124 ARG 0.008 0.001 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 2.523 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8245 (mmm) cc_final: 0.7961 (mmt) REVERT: B 295 GLU cc_start: 0.8171 (tt0) cc_final: 0.7815 (tt0) REVERT: C 133 ASP cc_start: 0.7933 (t70) cc_final: 0.7667 (p0) REVERT: D 171 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.8038 (mpt90) REVERT: D 309 MET cc_start: 0.8877 (mtp) cc_final: 0.8584 (mtp) REVERT: E 163 MET cc_start: 0.7814 (tpp) cc_final: 0.7611 (tpp) REVERT: E 272 MET cc_start: 0.8050 (mtt) cc_final: 0.7573 (mtt) REVERT: F 211 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8197 (ttp-110) REVERT: F 267 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8010 (ttp-110) REVERT: F 295 GLU cc_start: 0.7801 (tt0) cc_final: 0.7166 (tt0) outliers start: 26 outliers final: 22 residues processed: 266 average time/residue: 0.7408 time to fit residues: 278.9528 Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 128 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16603 Z= 0.187 Angle : 0.525 8.919 22607 Z= 0.266 Chirality : 0.039 0.154 2552 Planarity : 0.004 0.046 2808 Dihedral : 14.073 137.704 2590 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.34 % Allowed : 9.63 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.16 (0.19), residues: 1950 helix: 1.21 (0.17), residues: 1045 sheet: 0.61 (0.29), residues: 302 loop : 0.28 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 146 PHE 0.008 0.001 PHE B 58 TYR 0.015 0.001 TYR C 124 ARG 0.006 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.293 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8229 (mmm) cc_final: 0.7953 (mmt) REVERT: B 236 ASP cc_start: 0.7455 (t0) cc_final: 0.7208 (t0) REVERT: B 295 GLU cc_start: 0.8166 (tt0) cc_final: 0.7867 (tt0) REVERT: C 133 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7618 (p0) REVERT: C 135 MET cc_start: 0.4209 (mmm) cc_final: 0.3931 (mmm) REVERT: D 171 ARG cc_start: 0.8402 (mmt-90) cc_final: 0.8007 (mpt90) REVERT: D 309 MET cc_start: 0.8846 (mtp) cc_final: 0.8559 (mtp) REVERT: E 163 MET cc_start: 0.7805 (tpp) cc_final: 0.7599 (tpp) REVERT: E 272 MET cc_start: 0.8016 (mtt) cc_final: 0.7544 (mtt) REVERT: F 211 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8194 (ttp-110) REVERT: F 267 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8005 (ttp-110) REVERT: F 295 GLU cc_start: 0.7772 (tt0) cc_final: 0.7141 (tt0) outliers start: 22 outliers final: 20 residues processed: 263 average time/residue: 0.7575 time to fit residues: 281.3651 Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16603 Z= 0.202 Angle : 0.523 6.898 22607 Z= 0.265 Chirality : 0.039 0.153 2552 Planarity : 0.004 0.044 2808 Dihedral : 14.037 141.807 2590 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.46 % Allowed : 9.75 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.18 (0.19), residues: 1950 helix: 1.26 (0.17), residues: 1049 sheet: 0.59 (0.29), residues: 301 loop : 0.24 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 146 PHE 0.007 0.001 PHE B 58 TYR 0.015 0.001 TYR C 124 ARG 0.007 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 2.691 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: symmetry clash REVERT: A 163 MET cc_start: 0.8240 (mmm) cc_final: 0.7964 (mmt) REVERT: B 295 GLU cc_start: 0.8160 (tt0) cc_final: 0.7857 (tt0) REVERT: C 133 ASP cc_start: 0.7822 (t70) cc_final: 0.7621 (p0) REVERT: C 135 MET cc_start: 0.4286 (mmm) cc_final: 0.3903 (mmm) REVERT: D 171 ARG cc_start: 0.8391 (mmt-90) cc_final: 0.7997 (mpt90) REVERT: D 309 MET cc_start: 0.8850 (mtp) cc_final: 0.8569 (mtp) REVERT: E 163 MET cc_start: 0.7806 (tpp) cc_final: 0.7599 (tpp) REVERT: E 272 MET cc_start: 0.8024 (mtt) cc_final: 0.7555 (mtt) REVERT: F 211 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8207 (ttp-110) REVERT: F 267 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.8020 (ttp-110) REVERT: F 295 GLU cc_start: 0.7779 (tt0) cc_final: 0.7133 (tt0) outliers start: 24 outliers final: 22 residues processed: 256 average time/residue: 0.7545 time to fit residues: 273.1587 Evaluate side-chains 260 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16603 Z= 0.231 Angle : 0.535 6.497 22607 Z= 0.272 Chirality : 0.039 0.153 2552 Planarity : 0.004 0.047 2808 Dihedral : 14.048 142.419 2590 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.65 % Allowed : 9.57 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1950 helix: 1.20 (0.17), residues: 1051 sheet: 0.56 (0.30), residues: 301 loop : 0.14 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 146 PHE 0.008 0.001 PHE C 58 TYR 0.017 0.001 TYR C 124 ARG 0.007 0.000 ARG F 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 2.378 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: symmetry clash REVERT: A 163 MET cc_start: 0.8228 (mmm) cc_final: 0.7947 (mmt) REVERT: B 295 GLU cc_start: 0.8154 (tt0) cc_final: 0.7857 (tt0) REVERT: D 171 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.7986 (mpt90) REVERT: D 309 MET cc_start: 0.8860 (mtp) cc_final: 0.8599 (mtp) REVERT: E 163 MET cc_start: 0.7832 (tpp) cc_final: 0.7618 (tpp) REVERT: E 272 MET cc_start: 0.8063 (mtt) cc_final: 0.7602 (mtt) REVERT: F 211 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8191 (ttp-110) REVERT: F 267 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8037 (ttp-110) REVERT: F 295 GLU cc_start: 0.7741 (tt0) cc_final: 0.7105 (tt0) REVERT: H 200 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7300 (ttp80) outliers start: 27 outliers final: 25 residues processed: 258 average time/residue: 0.7266 time to fit residues: 267.2279 Evaluate side-chains 264 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 211 ARG Chi-restraints excluded: chain G residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 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 246 GLN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087490 restraints weight = 69901.960| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.24 r_work: 0.2855 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16603 Z= 0.206 Angle : 0.533 11.678 22607 Z= 0.270 Chirality : 0.039 0.151 2552 Planarity : 0.004 0.047 2808 Dihedral : 14.012 143.957 2590 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.52 % Allowed : 9.93 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.14 (0.19), residues: 1950 helix: 1.27 (0.17), residues: 1049 sheet: 0.59 (0.30), residues: 298 loop : 0.13 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 146 PHE 0.008 0.001 PHE C 58 TYR 0.015 0.001 TYR C 124 ARG 0.007 0.000 ARG F 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7785.25 seconds wall clock time: 137 minutes 31.95 seconds (8251.95 seconds total)