Starting phenix.real_space_refine on Wed Feb 21 22:16:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbm_13295/02_2024/7pbm_13295_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbm_13295/02_2024/7pbm_13295.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/7pbm_13295/02_2024/7pbm_13295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbm_13295/02_2024/7pbm_13295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbm_13295/02_2024/7pbm_13295_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbm_13295/02_2024/7pbm_13295_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 45 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3220 1.98 5 H 15819 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32079 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: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} 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: 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: 13.79, per 1000 atoms: 0.43 Number of scatterers: 32079 At special positions: 0 Unit cell: (125.35, 137.34, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 45 15.00 Mg 3 11.99 O 3220 8.00 N 2757 7.00 C 10134 6.00 H 15819 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: 26.21 Conformation dependent library (CDL) restraints added in 3.3 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: 106 helices and 17 sheets defined 49.8% alpha, 10.5% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 16.12 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.554A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.606A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.630A 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 126 removed outlier: 4.419A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 169 No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.670A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.917A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.551A pdb=" N GLN A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.868A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.626A 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 removed outlier: 3.637A pdb=" N MET A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.568A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.671A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (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: 4.916A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.881A 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 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.799A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 removed outlier: 3.525A pdb=" N HIS B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) 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: 3.753A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.802A 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: 3.575A pdb=" N GLU C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.713A 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 171 removed outlier: 3.534A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 171' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.590A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 210 removed outlier: 3.581A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.531A pdb=" N TYR C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.657A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.554A 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 removed outlier: 3.504A pdb=" N GLU C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.727A 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: 3.790A 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 128 removed outlier: 4.673A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.944A 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 removed outlier: 3.725A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 4.457A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 4.043A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.525A pdb=" N ARG D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.515A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.687A 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: 3.627A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.643A 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 117 through 129 removed outlier: 3.719A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.048A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.501A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 212 removed outlier: 3.769A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.927A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 removed outlier: 3.596A 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: 3.622A 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 32 through 47 removed outlier: 3.504A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.593A 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: 3.963A 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: 4.529A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 166 through 169 No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 217 through 233 removed outlier: 4.084A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.891A pdb=" N GLU F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 291 through 297 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 177 removed outlier: 3.667A pdb=" N ALA A 157 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.548A 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 removed outlier: 3.506A pdb=" N ILE A 136 " --> pdb=" O ARG A 143 " (cutoff:3.500A) 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 178 removed outlier: 3.733A pdb=" N GLY B 59 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.515A pdb=" N ASP C 110 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 131 through 136 Processing sheet with id= I, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= K, first strand: chain 'D' and resid 131 through 136 Processing sheet with id= L, first strand: chain 'E' and resid 174 through 177 removed outlier: 3.515A pdb=" N ALA E 157 " --> pdb=" O ILE E 109 " (cutoff:3.500A) 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 removed outlier: 3.521A pdb=" N ILE F 134 " --> pdb=" O VAL F 145 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 308 through 311 632 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.11 Time building geometry restraints manager: 26.96 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: 15819 1.06 - 1.28: 2721 1.28 - 1.50: 6908 1.50 - 1.72: 6779 1.72 - 1.94: 199 Bond restraints: 32426 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 E 19 " pdb=" H1 THR E 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 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 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 2.50e+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 ... (remaining 32421 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.85: 802 106.85 - 114.24: 39585 114.24 - 121.64: 12545 121.64 - 129.03: 5685 129.03 - 136.43: 75 Bond angle restraints: 58692 Sorted by residual: angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.41 105.10 5.31 1.23e+00 6.61e-01 1.86e+01 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 120.24 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" N PHE D 197 " pdb=" CA PHE D 197 " pdb=" C PHE D 197 " ideal model delta sigma weight residual 110.41 106.11 4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.83 10.17 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 108.00 117.22 -9.22 3.00e+00 1.11e-01 9.44e+00 ... (remaining 58687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 14436 32.07 - 64.14: 566 64.14 - 96.21: 32 96.21 - 128.28: 2 128.28 - 160.35: 4 Dihedral angle restraints: 15040 sinusoidal: 8607 harmonic: 6433 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 -60.00 100.36 -160.35 1 2.00e+01 2.50e-03 4.66e+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 86.89 -146.89 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.64 -136.65 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 15037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2317 0.077 - 0.153: 233 0.153 - 0.230: 3 0.230 - 0.306: 0 0.306 - 0.383: 1 Chirality restraints: 2554 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 -2.73 -0.38 2.00e-01 2.50e+01 3.67e+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 2.32 0.19 2.00e-01 2.50e+01 8.72e-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 8.53e-01 ... (remaining 2551 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.156 9.50e-02 1.11e+02 7.14e-02 5.63e+01 pdb=" NE ARG C 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.082 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.067 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 312 " -0.445 9.50e-02 1.11e+02 1.53e-01 5.48e+01 pdb=" NE ARG F 312 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 312 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG F 312 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG F 312 " 0.062 2.00e-02 2.50e+03 pdb="HH11 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG F 312 " -0.037 2.00e-02 2.50e+03 pdb="HH21 ARG F 312 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 312 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.044 2.00e-02 2.50e+03 5.51e-02 4.55e+01 pdb=" CD GLN C 31 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.088 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.085 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1089 2.17 - 2.78: 60828 2.78 - 3.39: 82594 3.39 - 3.99: 107747 3.99 - 4.60: 172616 Nonbonded interactions: 424874 Sorted by model distance: nonbonded pdb="HH21 ARG E 312 " pdb=" OP1 DA V 10 " model vdw 1.564 1.850 nonbonded pdb=" OE2 GLU C 128 " pdb="HH22 ARG D 218 " model vdw 1.570 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.570 1.850 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.591 1.850 nonbonded pdb=" O ALA F 138 " pdb=" HG1 THR F 141 " model vdw 1.593 1.850 ... (remaining 424869 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: 1.910 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: 0.430 Extract box with map and model: 10.790 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 110.250 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16607 Z= 0.255 Angle : 0.716 10.167 22614 Z= 0.409 Chirality : 0.044 0.383 2554 Planarity : 0.011 0.154 2808 Dihedral : 14.991 160.355 6412 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % 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: -1.25 (0.18), residues: 1950 helix: -1.47 (0.14), residues: 1035 sheet: 0.35 (0.30), residues: 298 loop : 0.22 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS A 324 PHE 0.019 0.003 PHE F 25 TYR 0.033 0.005 TYR F 131 ARG 0.031 0.003 ARG C 114 *********************** 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 428 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 2.661 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: A 76 MET cc_start: 0.9007 (mmm) cc_final: 0.8648 (mmt) REVERT: A 79 ASN cc_start: 0.7865 (m-40) cc_final: 0.7274 (m-40) REVERT: A 110 ASP cc_start: 0.8071 (t0) cc_final: 0.7844 (t70) REVERT: A 178 MET cc_start: 0.9017 (mmm) cc_final: 0.8766 (mmt) REVERT: A 222 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7478 (ttm170) REVERT: A 309 MET cc_start: 0.7229 (ttm) cc_final: 0.7017 (ttp) REVERT: C 121 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 144 SER cc_start: 0.6230 (p) cc_final: 0.5753 (p) REVERT: C 178 MET cc_start: 0.9112 (mmt) cc_final: 0.8637 (mmt) REVERT: C 234 MET cc_start: 0.8723 (mmt) cc_final: 0.8435 (mmt) REVERT: C 325 MET cc_start: 0.9365 (mmm) cc_final: 0.9162 (mmp) REVERT: D 105 ASP cc_start: 0.7600 (m-30) cc_final: 0.7168 (m-30) REVERT: E 105 ASP cc_start: 0.6662 (m-30) cc_final: 0.6107 (m-30) REVERT: E 330 THR cc_start: 0.7829 (m) cc_final: 0.7550 (p) REVERT: F 102 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7400 (mm-30) REVERT: F 298 TYR cc_start: 0.7431 (m-80) cc_final: 0.7201 (m-80) REVERT: H 200 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7509 (mmm-85) outliers start: 1 outliers final: 1 residues processed: 428 average time/residue: 0.7682 time to fit residues: 454.8781 Evaluate side-chains 263 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.238 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 GLN D 286 ASN G 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16607 Z= 0.290 Angle : 0.621 6.031 22614 Z= 0.334 Chirality : 0.042 0.134 2554 Planarity : 0.005 0.042 2808 Dihedral : 14.525 157.835 2599 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.28 % Allowed : 6.15 % Favored : 92.57 % 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: -0.11 (0.18), residues: 1950 helix: -0.06 (0.16), residues: 1027 sheet: 0.12 (0.29), residues: 307 loop : 0.19 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.011 0.001 PHE B 58 TYR 0.030 0.001 TYR C 124 ARG 0.004 0.001 ARG B 218 *********************** 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 290 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 269 time to evaluate : 2.591 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 76 MET cc_start: 0.8885 (mmm) cc_final: 0.8567 (mmt) REVERT: A 79 ASN cc_start: 0.7846 (m-40) cc_final: 0.7274 (m-40) REVERT: A 204 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 222 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7350 (ttm170) REVERT: C 110 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: C 121 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 147 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7570 (mp) REVERT: C 178 MET cc_start: 0.9081 (mmt) cc_final: 0.8518 (mmt) REVERT: E 325 MET cc_start: 0.7843 (mmm) cc_final: 0.7549 (mmp) REVERT: E 330 THR cc_start: 0.7960 (m) cc_final: 0.7711 (p) REVERT: F 102 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7608 (mm-30) REVERT: G 167 LEU cc_start: 0.8117 (tp) cc_final: 0.7895 (tp) REVERT: H 200 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7585 (mtp-110) outliers start: 21 outliers final: 13 residues processed: 280 average time/residue: 0.7742 time to fit residues: 307.6715 Evaluate side-chains 265 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16607 Z= 0.240 Angle : 0.552 6.367 22614 Z= 0.292 Chirality : 0.040 0.192 2554 Planarity : 0.004 0.046 2808 Dihedral : 14.431 155.279 2599 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.91 % Allowed : 7.68 % Favored : 91.41 % 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: 0.23 (0.19), residues: 1950 helix: 0.36 (0.17), residues: 1028 sheet: 0.05 (0.28), residues: 307 loop : 0.17 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.008 0.001 PHE B 58 TYR 0.022 0.001 TYR C 124 ARG 0.009 0.000 ARG A 143 *********************** 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 267 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.678 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 76 MET cc_start: 0.8827 (mmm) cc_final: 0.8520 (mmt) REVERT: A 79 ASN cc_start: 0.7821 (m-40) cc_final: 0.7250 (m-40) REVERT: A 222 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7451 (ttm170) REVERT: C 147 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 178 MET cc_start: 0.9061 (mmt) cc_final: 0.8539 (mmt) REVERT: E 81 LYS cc_start: 0.7737 (mttt) cc_final: 0.6987 (tptt) REVERT: E 330 THR cc_start: 0.8058 (m) cc_final: 0.7781 (p) REVERT: F 102 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7712 (mm-30) REVERT: G 167 LEU cc_start: 0.8112 (tp) cc_final: 0.7889 (tp) REVERT: H 200 ARG cc_start: 0.7836 (ttt180) cc_final: 0.7549 (mtp-110) outliers start: 15 outliers final: 10 residues processed: 261 average time/residue: 0.7619 time to fit residues: 277.8803 Evaluate side-chains 256 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 189 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16607 Z= 0.189 Angle : 0.521 6.134 22614 Z= 0.272 Chirality : 0.039 0.129 2554 Planarity : 0.004 0.044 2808 Dihedral : 14.323 150.295 2599 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.04 % Allowed : 7.92 % Favored : 91.04 % 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: 0.52 (0.19), residues: 1950 helix: 0.68 (0.17), residues: 1032 sheet: 0.04 (0.28), residues: 303 loop : 0.21 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.008 0.001 PHE B 58 TYR 0.020 0.001 TYR C 124 ARG 0.005 0.000 ARG G 179 *********************** 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 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8718 (mmm) cc_final: 0.8417 (mmt) REVERT: A 79 ASN cc_start: 0.7909 (m-40) cc_final: 0.7363 (m-40) REVERT: A 222 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7463 (ttm170) REVERT: A 290 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6494 (tt0) REVERT: C 147 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7615 (mp) REVERT: C 178 MET cc_start: 0.9038 (mmt) cc_final: 0.8499 (mmt) REVERT: E 81 LYS cc_start: 0.7735 (mttt) cc_final: 0.6976 (tptt) REVERT: E 325 MET cc_start: 0.7843 (mmm) cc_final: 0.7598 (mmp) REVERT: E 330 THR cc_start: 0.8056 (m) cc_final: 0.7783 (p) REVERT: F 68 MET cc_start: 0.8726 (tpp) cc_final: 0.8428 (tpp) REVERT: F 102 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7718 (mm-30) REVERT: G 167 LEU cc_start: 0.8089 (tp) cc_final: 0.7876 (tp) REVERT: H 200 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7529 (mtp-110) outliers start: 17 outliers final: 14 residues processed: 259 average time/residue: 0.8133 time to fit residues: 298.3872 Evaluate side-chains 259 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 284 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16607 Z= 0.229 Angle : 0.524 6.346 22614 Z= 0.273 Chirality : 0.040 0.130 2554 Planarity : 0.004 0.046 2808 Dihedral : 14.247 147.569 2599 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 8.65 % Favored : 90.01 % 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: 0.61 (0.19), residues: 1950 helix: 0.79 (0.17), residues: 1028 sheet: -0.03 (0.28), residues: 302 loop : 0.25 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 146 PHE 0.010 0.001 PHE C 108 TYR 0.021 0.001 TYR C 124 ARG 0.003 0.000 ARG C 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 272 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 250 time to evaluate : 2.439 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 76 MET cc_start: 0.8694 (mmm) cc_final: 0.8458 (mmt) REVERT: A 79 ASN cc_start: 0.7894 (m-40) cc_final: 0.7345 (m-40) REVERT: A 222 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7500 (ttm170) REVERT: A 290 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6653 (tt0) REVERT: C 147 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 178 MET cc_start: 0.9035 (mmt) cc_final: 0.8478 (mmt) REVERT: D 120 GLU cc_start: 0.7528 (tt0) cc_final: 0.7120 (tt0) REVERT: E 81 LYS cc_start: 0.7794 (mttt) cc_final: 0.6977 (tptt) REVERT: E 330 THR cc_start: 0.8086 (m) cc_final: 0.7813 (p) REVERT: F 102 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7712 (mm-30) REVERT: G 167 LEU cc_start: 0.8097 (tp) cc_final: 0.7892 (tp) REVERT: H 200 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7535 (mtp-110) outliers start: 22 outliers final: 19 residues processed: 260 average time/residue: 0.7697 time to fit residues: 280.5029 Evaluate side-chains 264 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain G residue 191 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16607 Z= 0.179 Angle : 0.502 6.194 22614 Z= 0.259 Chirality : 0.039 0.126 2554 Planarity : 0.004 0.043 2808 Dihedral : 14.114 148.514 2599 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.22 % Allowed : 8.78 % Favored : 90.01 % 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: 0.83 (0.19), residues: 1950 helix: 0.96 (0.17), residues: 1035 sheet: 0.09 (0.28), residues: 300 loop : 0.36 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.012 0.001 PHE C 108 TYR 0.018 0.001 TYR C 124 ARG 0.005 0.000 ARG A 160 *********************** 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 268 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8707 (mmm) cc_final: 0.8473 (mmt) REVERT: A 79 ASN cc_start: 0.7865 (m-40) cc_final: 0.7309 (m-40) REVERT: A 222 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7519 (ttm170) REVERT: A 290 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6722 (tt0) REVERT: C 147 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7609 (mp) REVERT: C 178 MET cc_start: 0.9026 (mmt) cc_final: 0.8463 (mmt) REVERT: D 120 GLU cc_start: 0.7512 (tt0) cc_final: 0.7086 (tt0) REVERT: D 135 MET cc_start: 0.7567 (mmt) cc_final: 0.7299 (mmt) REVERT: E 81 LYS cc_start: 0.7801 (mttt) cc_final: 0.6954 (tptt) REVERT: E 117 MET cc_start: 0.7244 (tpp) cc_final: 0.6913 (tpt) REVERT: E 330 THR cc_start: 0.8083 (m) cc_final: 0.7816 (p) REVERT: F 102 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7706 (mm-30) REVERT: G 167 LEU cc_start: 0.8094 (tp) cc_final: 0.7888 (tp) REVERT: H 200 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7513 (mtp-110) outliers start: 20 outliers final: 13 residues processed: 259 average time/residue: 0.7833 time to fit residues: 288.0960 Evaluate side-chains 254 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 284 SER 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: 2.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16607 Z= 0.252 Angle : 0.527 6.250 22614 Z= 0.273 Chirality : 0.040 0.126 2554 Planarity : 0.004 0.048 2808 Dihedral : 14.117 148.018 2599 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.16 % Allowed : 9.26 % Favored : 89.58 % 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: 0.71 (0.19), residues: 1950 helix: 0.94 (0.17), residues: 1029 sheet: -0.00 (0.28), residues: 302 loop : 0.18 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 146 PHE 0.009 0.001 PHE C 108 TYR 0.020 0.001 TYR C 124 ARG 0.004 0.000 ARG A 160 *********************** 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 260 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 241 time to evaluate : 2.308 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 79 ASN cc_start: 0.7852 (m-40) cc_final: 0.7291 (m-40) REVERT: A 222 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7503 (ttm170) REVERT: A 290 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6883 (tt0) REVERT: C 147 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7621 (mp) REVERT: D 120 GLU cc_start: 0.7472 (tt0) cc_final: 0.7068 (tt0) REVERT: D 135 MET cc_start: 0.7658 (mmt) cc_final: 0.7425 (mmt) REVERT: E 81 LYS cc_start: 0.7823 (mttt) cc_final: 0.6941 (tptt) REVERT: E 117 MET cc_start: 0.7232 (tpp) cc_final: 0.6952 (tpt) REVERT: E 330 THR cc_start: 0.8063 (m) cc_final: 0.7798 (p) REVERT: F 102 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7724 (mm-30) REVERT: G 167 LEU cc_start: 0.8124 (tp) cc_final: 0.7915 (tp) REVERT: H 200 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7481 (mtp-110) outliers start: 19 outliers final: 16 residues processed: 250 average time/residue: 0.7807 time to fit residues: 272.9713 Evaluate side-chains 258 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 191 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16607 Z= 0.222 Angle : 0.516 6.052 22614 Z= 0.267 Chirality : 0.039 0.132 2554 Planarity : 0.004 0.048 2808 Dihedral : 14.074 148.309 2599 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.16 % Allowed : 9.63 % Favored : 89.21 % 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: 0.77 (0.19), residues: 1950 helix: 1.01 (0.17), residues: 1033 sheet: 0.00 (0.28), residues: 302 loop : 0.18 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 146 PHE 0.009 0.001 PHE C 108 TYR 0.019 0.001 TYR C 124 ARG 0.005 0.000 ARG E 312 *********************** 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 266 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 2.670 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 79 ASN cc_start: 0.7821 (m-40) cc_final: 0.7269 (m-40) REVERT: A 222 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7552 (ttm170) REVERT: C 147 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7618 (mp) REVERT: C 178 MET cc_start: 0.9026 (mmt) cc_final: 0.8457 (mmt) REVERT: D 105 ASP cc_start: 0.7532 (m-30) cc_final: 0.7097 (m-30) REVERT: D 120 GLU cc_start: 0.7492 (tt0) cc_final: 0.7082 (tt0) REVERT: D 135 MET cc_start: 0.7623 (mmt) cc_final: 0.7374 (mmt) REVERT: E 81 LYS cc_start: 0.7729 (mttt) cc_final: 0.6883 (tptt) REVERT: E 117 MET cc_start: 0.7238 (tpp) cc_final: 0.6975 (tpt) REVERT: E 330 THR cc_start: 0.8060 (m) cc_final: 0.7795 (p) REVERT: F 102 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7725 (mm-30) REVERT: G 167 LEU cc_start: 0.8112 (tp) cc_final: 0.7904 (tp) REVERT: H 200 ARG cc_start: 0.7729 (ttt180) cc_final: 0.7472 (mtp-110) outliers start: 19 outliers final: 17 residues processed: 258 average time/residue: 0.7858 time to fit residues: 287.4841 Evaluate side-chains 259 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 191 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16607 Z= 0.234 Angle : 0.519 6.006 22614 Z= 0.268 Chirality : 0.040 0.124 2554 Planarity : 0.004 0.050 2808 Dihedral : 14.042 148.430 2599 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.16 % Allowed : 9.75 % Favored : 89.09 % 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: 0.77 (0.19), residues: 1950 helix: 1.04 (0.17), residues: 1031 sheet: -0.03 (0.28), residues: 302 loop : 0.14 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.009 0.001 PHE C 108 TYR 0.019 0.001 TYR C 124 ARG 0.006 0.000 ARG A 160 *********************** 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: 19 poor density : 245 time to evaluate : 2.432 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 79 ASN cc_start: 0.7810 (m-40) cc_final: 0.7254 (m-40) REVERT: A 222 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7489 (ttm170) REVERT: C 147 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 178 MET cc_start: 0.9019 (mmt) cc_final: 0.8446 (mmt) REVERT: D 120 GLU cc_start: 0.7508 (tt0) cc_final: 0.7115 (tt0) REVERT: D 135 MET cc_start: 0.7613 (mmt) cc_final: 0.7346 (mmt) REVERT: E 81 LYS cc_start: 0.7729 (mttt) cc_final: 0.6859 (tptt) REVERT: E 117 MET cc_start: 0.7283 (tpp) cc_final: 0.7033 (tpt) REVERT: E 330 THR cc_start: 0.8080 (m) cc_final: 0.7810 (p) REVERT: F 102 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7740 (mm-30) REVERT: G 167 LEU cc_start: 0.8099 (tp) cc_final: 0.7899 (tp) REVERT: H 200 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7468 (mtp-110) outliers start: 19 outliers final: 17 residues processed: 256 average time/residue: 0.7782 time to fit residues: 277.6001 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 182 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.224 Angle : 0.518 6.027 22614 Z= 0.266 Chirality : 0.039 0.123 2554 Planarity : 0.004 0.048 2808 Dihedral : 14.013 148.693 2599 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.22 % Allowed : 9.75 % 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: 0.81 (0.19), residues: 1950 helix: 1.07 (0.17), residues: 1036 sheet: 0.00 (0.28), residues: 300 loop : 0.14 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 146 PHE 0.009 0.001 PHE C 108 TYR 0.019 0.001 TYR C 124 ARG 0.005 0.000 ARG A 160 ********************** 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 262 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 2.341 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 79 ASN cc_start: 0.7799 (m-40) cc_final: 0.7245 (m-40) REVERT: A 222 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7486 (ttm170) REVERT: C 147 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 178 MET cc_start: 0.9017 (mmt) cc_final: 0.8443 (mmt) REVERT: D 105 ASP cc_start: 0.7572 (m-30) cc_final: 0.7133 (m-30) REVERT: D 120 GLU cc_start: 0.7544 (tt0) cc_final: 0.7156 (tt0) REVERT: D 135 MET cc_start: 0.7590 (mmt) cc_final: 0.7291 (mmt) REVERT: E 81 LYS cc_start: 0.7747 (mttt) cc_final: 0.6838 (tptt) REVERT: E 117 MET cc_start: 0.7266 (tpp) cc_final: 0.7022 (tpt) REVERT: E 330 THR cc_start: 0.8088 (m) cc_final: 0.7819 (p) REVERT: F 102 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7750 (mm-30) REVERT: G 167 LEU cc_start: 0.8094 (tp) cc_final: 0.7893 (tp) REVERT: H 200 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7469 (mtp-110) outliers start: 20 outliers final: 18 residues processed: 254 average time/residue: 0.7827 time to fit residues: 281.2919 Evaluate side-chains 258 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 182 SER 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: 0.0470 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098162 restraints weight = 66118.124| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.16 r_work: 0.2887 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16607 Z= 0.209 Angle : 0.514 6.107 22614 Z= 0.264 Chirality : 0.039 0.125 2554 Planarity : 0.004 0.047 2808 Dihedral : 13.977 148.870 2599 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.16 % Allowed : 9.99 % Favored : 88.85 % 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: 0.86 (0.19), residues: 1950 helix: 1.12 (0.17), residues: 1035 sheet: -0.00 (0.28), residues: 299 loop : 0.15 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 146 PHE 0.008 0.001 PHE C 108 TYR 0.019 0.001 TYR C 124 ARG 0.005 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7820.41 seconds wall clock time: 138 minutes 27.30 seconds (8307.30 seconds total)