Starting phenix.real_space_refine on Sat Jul 26 05:57:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpg_27634/07_2025/8dpg_27634_trim.cif" } resolution = 3.6 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= 0.002 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5237 2.51 5 N 1369 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8162 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1939 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'91Q': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.08, per 1000 atoms: 0.62 Number of scatterers: 8162 At special positions: 0 Unit cell: (89.18, 119.21, 133.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1500 8.00 N 1369 7.00 C 5237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 39.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.520A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.010A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.561A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.210A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.693A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.928A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.006A pdb=" N VAL A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.454A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.329A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.584A pdb=" N ILE A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.753A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.895A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.590A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.099A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.626A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.957A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.591A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.526A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.595A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.581A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.583A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.846A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.006A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.030A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.911A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.983A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.727A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.150A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.845A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.180A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.180A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.521A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2619 1.34 - 1.46: 2014 1.46 - 1.58: 3614 1.58 - 1.70: 0 1.70 - 1.81: 83 Bond restraints: 8330 Sorted by residual: bond pdb=" C6 91Q A 501 " pdb=" N2 91Q A 501 " ideal model delta sigma weight residual 1.368 1.310 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" C7 91Q A 501 " pdb=" C8 91Q A 501 " ideal model delta sigma weight residual 1.412 1.357 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C9 91Q A 501 " pdb=" O1 91Q A 501 " ideal model delta sigma weight residual 1.349 1.394 -0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" C4 91Q A 501 " pdb=" C5 91Q A 501 " ideal model delta sigma weight residual 1.494 1.522 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C5 91Q A 501 " pdb=" C8 91Q A 501 " ideal model delta sigma weight residual 1.437 1.412 0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 8325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11286 2.30 - 4.60: 59 4.60 - 6.89: 7 6.89 - 9.19: 0 9.19 - 11.49: 2 Bond angle restraints: 11354 Sorted by residual: angle pdb=" C1 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C3 91Q A 501 " ideal model delta sigma weight residual 111.25 122.74 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA LEU A 370 " pdb=" CB LEU A 370 " pdb=" CG LEU A 370 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.88e+00 angle pdb=" N VAL A 352 " pdb=" CA VAL A 352 " pdb=" C VAL A 352 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.82e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" C MET E 180 " ideal model delta sigma weight residual 110.80 115.46 -4.66 2.13e+00 2.20e-01 4.79e+00 ... (remaining 11349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.60: 4860 28.60 - 57.21: 44 57.21 - 85.81: 7 85.81 - 114.42: 0 114.42 - 143.02: 2 Dihedral angle restraints: 4913 sinusoidal: 1749 harmonic: 3164 Sorted by residual: dihedral pdb=" C1 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual -162.00 -18.98 -143.02 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C2 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 73.77 -152.43 -133.80 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 4910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.075: 295 0.075 - 0.113: 89 0.113 - 0.150: 19 0.150 - 0.188: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" C17 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C16 CLR A 502 " pdb=" C20 CLR A 502 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1342 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO C 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 364 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 365 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 91Q A 501 " 0.003 2.00e-02 2.50e+03 6.35e-03 1.11e+00 pdb=" C11 91Q A 501 " 0.013 2.00e-02 2.50e+03 pdb=" C12 91Q A 501 " -0.005 2.00e-02 2.50e+03 pdb=" C4 91Q A 501 " 0.004 2.00e-02 2.50e+03 pdb=" C5 91Q A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C6 91Q A 501 " 0.001 2.00e-02 2.50e+03 pdb=" C7 91Q A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C8 91Q A 501 " -0.001 2.00e-02 2.50e+03 pdb=" C9 91Q A 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 91Q A 501 " -0.004 2.00e-02 2.50e+03 pdb=" O1 91Q A 501 " -0.006 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 130 2.70 - 3.25: 7506 3.25 - 3.80: 11937 3.80 - 4.35: 15434 4.35 - 4.90: 27077 Nonbonded interactions: 62084 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.264 3.120 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.264 3.040 ... (remaining 62079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 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 : 0.003 0.231 8333 Z= 0.277 Angle : 0.487 11.489 11358 Z= 0.260 Chirality : 0.041 0.188 1345 Planarity : 0.003 0.035 1424 Dihedral : 9.689 143.022 2859 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.61 % Allowed : 1.59 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.82 (0.26), residues: 1065 helix: 2.15 (0.29), residues: 332 sheet: 1.44 (0.30), residues: 292 loop : 0.40 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 130 HIS 0.004 0.001 HIS B 209 PHE 0.009 0.001 PHE C 199 TYR 0.008 0.001 TYR E 102 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.21935 ( 399) hydrogen bonds : angle 6.10371 ( 1125) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.84401 ( 4) covalent geometry : bond 0.00218 ( 8330) covalent geometry : angle 0.48664 (11354) Misc. bond : bond 0.23092 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.7304 (tttt) cc_final: 0.7033 (tttt) REVERT: C 61 MET cc_start: 0.7443 (tmm) cc_final: 0.6947 (tmm) REVERT: C 68 ARG cc_start: 0.7583 (mtp180) cc_final: 0.6620 (mtp180) REVERT: C 70 LEU cc_start: 0.6940 (tt) cc_final: 0.6707 (tp) REVERT: C 86 THR cc_start: 0.7691 (p) cc_final: 0.7400 (p) REVERT: C 130 GLU cc_start: 0.7079 (mp0) cc_final: 0.6756 (mp0) REVERT: C 135 VAL cc_start: 0.7991 (t) cc_final: 0.7752 (p) REVERT: C 243 THR cc_start: 0.7434 (t) cc_final: 0.7209 (p) REVERT: C 292 PHE cc_start: 0.7578 (m-10) cc_final: 0.7361 (m-80) REVERT: C 334 SER cc_start: 0.8135 (m) cc_final: 0.7466 (t) REVERT: E 98 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7256 (ptt180) REVERT: E 106 SER cc_start: 0.8469 (t) cc_final: 0.8072 (p) REVERT: E 162 LEU cc_start: 0.8462 (tp) cc_final: 0.8149 (tp) outliers start: 5 outliers final: 1 residues processed: 182 average time/residue: 0.2193 time to fit residues: 53.8486 Evaluate side-chains 140 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127577 restraints weight = 11505.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129929 restraints weight = 7674.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131269 restraints weight = 5743.522| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8333 Z= 0.145 Angle : 0.550 7.144 11358 Z= 0.295 Chirality : 0.044 0.150 1345 Planarity : 0.004 0.038 1424 Dihedral : 6.771 78.650 1231 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.44 % Allowed : 7.80 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.83 (0.26), residues: 1065 helix: 2.17 (0.30), residues: 353 sheet: 1.63 (0.31), residues: 274 loop : 0.21 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 130 HIS 0.006 0.001 HIS B 209 PHE 0.014 0.002 PHE B 100 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 399) hydrogen bonds : angle 4.39373 ( 1125) SS BOND : bond 0.00585 ( 2) SS BOND : angle 1.58668 ( 4) covalent geometry : bond 0.00322 ( 8330) covalent geometry : angle 0.54904 (11354) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.840 Fit side-chains REVERT: B 195 LYS cc_start: 0.7275 (tttt) cc_final: 0.7016 (tttt) REVERT: C 61 MET cc_start: 0.7421 (tmm) cc_final: 0.6833 (tmm) REVERT: C 68 ARG cc_start: 0.7472 (mtp180) cc_final: 0.6593 (mtp180) REVERT: C 86 THR cc_start: 0.7969 (p) cc_final: 0.7694 (p) REVERT: C 135 VAL cc_start: 0.8055 (t) cc_final: 0.7824 (p) REVERT: C 252 LEU cc_start: 0.8547 (tp) cc_final: 0.8198 (tt) REVERT: C 292 PHE cc_start: 0.7414 (m-10) cc_final: 0.7148 (m-80) REVERT: C 334 SER cc_start: 0.8206 (m) cc_final: 0.7616 (t) REVERT: E 98 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7175 (ptt180) REVERT: E 106 SER cc_start: 0.8595 (t) cc_final: 0.8266 (p) outliers start: 20 outliers final: 9 residues processed: 155 average time/residue: 0.2166 time to fit residues: 45.8301 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 78 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 119 ASN C 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126177 restraints weight = 11725.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128460 restraints weight = 7748.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129969 restraints weight = 5813.747| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8333 Z= 0.124 Angle : 0.518 8.892 11358 Z= 0.275 Chirality : 0.043 0.154 1345 Planarity : 0.004 0.038 1424 Dihedral : 6.267 58.828 1230 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.95 % Allowed : 11.10 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.97 (0.27), residues: 1065 helix: 2.49 (0.30), residues: 343 sheet: 1.63 (0.31), residues: 274 loop : 0.19 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.014 0.002 PHE C 199 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 399) hydrogen bonds : angle 4.08377 ( 1125) SS BOND : bond 0.00582 ( 2) SS BOND : angle 1.35293 ( 4) covalent geometry : bond 0.00272 ( 8330) covalent geometry : angle 0.51772 (11354) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.932 Fit side-chains REVERT: A 350 LEU cc_start: 0.7046 (mt) cc_final: 0.6825 (tt) REVERT: B 110 VAL cc_start: 0.7852 (t) cc_final: 0.7467 (m) REVERT: C 61 MET cc_start: 0.7362 (tmm) cc_final: 0.6890 (tmm) REVERT: C 68 ARG cc_start: 0.7344 (mtp180) cc_final: 0.6383 (mtp180) REVERT: C 135 VAL cc_start: 0.8143 (t) cc_final: 0.7862 (p) REVERT: C 252 LEU cc_start: 0.8442 (tp) cc_final: 0.8185 (tt) REVERT: C 292 PHE cc_start: 0.7416 (m-10) cc_final: 0.7125 (m-80) REVERT: E 29 PHE cc_start: 0.7828 (t80) cc_final: 0.7621 (t80) REVERT: E 78 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7577 (m) REVERT: E 98 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7067 (ptt180) REVERT: E 106 SER cc_start: 0.8540 (t) cc_final: 0.8193 (p) REVERT: E 181 SER cc_start: 0.8073 (m) cc_final: 0.7822 (m) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.2031 time to fit residues: 42.9377 Evaluate side-chains 150 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.143173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124895 restraints weight = 11539.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126994 restraints weight = 7642.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128648 restraints weight = 5769.059| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8333 Z= 0.125 Angle : 0.515 7.643 11358 Z= 0.274 Chirality : 0.043 0.171 1345 Planarity : 0.004 0.035 1424 Dihedral : 5.902 56.401 1230 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.05 % Allowed : 11.71 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.88 (0.27), residues: 1065 helix: 2.46 (0.29), residues: 346 sheet: 1.58 (0.31), residues: 274 loop : 0.08 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.015 0.002 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 399) hydrogen bonds : angle 3.96967 ( 1125) SS BOND : bond 0.00521 ( 2) SS BOND : angle 0.98099 ( 4) covalent geometry : bond 0.00278 ( 8330) covalent geometry : angle 0.51437 (11354) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.837 Fit side-chains REVERT: A 93 MET cc_start: 0.6527 (tpp) cc_final: 0.6118 (tpt) REVERT: B 195 LYS cc_start: 0.7228 (tttt) cc_final: 0.6941 (tttt) REVERT: C 61 MET cc_start: 0.7384 (tmm) cc_final: 0.6997 (tmm) REVERT: C 68 ARG cc_start: 0.7398 (mtp180) cc_final: 0.6419 (mtp180) REVERT: C 135 VAL cc_start: 0.8167 (t) cc_final: 0.7825 (p) REVERT: C 252 LEU cc_start: 0.8476 (tp) cc_final: 0.8212 (tt) REVERT: C 292 PHE cc_start: 0.7436 (m-10) cc_final: 0.7100 (m-80) REVERT: E 18 ARG cc_start: 0.6782 (mmm-85) cc_final: 0.6554 (mmm-85) REVERT: E 78 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7617 (m) REVERT: E 98 ARG cc_start: 0.7537 (ttp-170) cc_final: 0.6983 (ttt180) REVERT: E 106 SER cc_start: 0.8550 (t) cc_final: 0.8188 (p) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.2042 time to fit residues: 43.3675 Evaluate side-chains 156 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123208 restraints weight = 11471.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125382 restraints weight = 7653.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126949 restraints weight = 5757.764| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8333 Z= 0.154 Angle : 0.542 9.910 11358 Z= 0.289 Chirality : 0.043 0.159 1345 Planarity : 0.004 0.039 1424 Dihedral : 5.838 54.642 1230 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.29 % Allowed : 12.56 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.74 (0.27), residues: 1065 helix: 2.36 (0.29), residues: 347 sheet: 1.52 (0.31), residues: 274 loop : -0.04 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.007 0.002 HIS B 209 PHE 0.019 0.002 PHE C 199 TYR 0.016 0.002 TYR E 178 ARG 0.005 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 399) hydrogen bonds : angle 4.01752 ( 1125) SS BOND : bond 0.00606 ( 2) SS BOND : angle 1.30442 ( 4) covalent geometry : bond 0.00359 ( 8330) covalent geometry : angle 0.54135 (11354) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.818 Fit side-chains REVERT: A 93 MET cc_start: 0.6516 (tpp) cc_final: 0.5925 (tpt) REVERT: A 332 ILE cc_start: 0.7678 (mm) cc_final: 0.7139 (tt) REVERT: B 195 LYS cc_start: 0.7229 (tttt) cc_final: 0.6994 (tttt) REVERT: C 61 MET cc_start: 0.7400 (tmm) cc_final: 0.7053 (tmm) REVERT: C 68 ARG cc_start: 0.7366 (mtp180) cc_final: 0.6366 (mtp180) REVERT: C 135 VAL cc_start: 0.8145 (t) cc_final: 0.7792 (p) REVERT: C 292 PHE cc_start: 0.7441 (m-10) cc_final: 0.7123 (m-10) REVERT: C 296 VAL cc_start: 0.8385 (t) cc_final: 0.8143 (m) REVERT: E 98 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6955 (ttt180) REVERT: E 106 SER cc_start: 0.8557 (t) cc_final: 0.8182 (p) REVERT: E 132 THR cc_start: 0.6641 (OUTLIER) cc_final: 0.6382 (m) outliers start: 27 outliers final: 23 residues processed: 158 average time/residue: 0.2210 time to fit residues: 47.7503 Evaluate side-chains 164 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120455 restraints weight = 11525.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122509 restraints weight = 7575.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124069 restraints weight = 5694.310| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8333 Z= 0.223 Angle : 0.621 10.099 11358 Z= 0.332 Chirality : 0.046 0.167 1345 Planarity : 0.004 0.052 1424 Dihedral : 6.150 54.969 1230 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.29 % Allowed : 13.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1065 helix: 2.05 (0.29), residues: 347 sheet: 1.39 (0.31), residues: 278 loop : -0.36 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 211 HIS 0.008 0.002 HIS B 209 PHE 0.024 0.003 PHE C 199 TYR 0.018 0.002 TYR E 95 ARG 0.006 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.06069 ( 399) hydrogen bonds : angle 4.32081 ( 1125) SS BOND : bond 0.00771 ( 2) SS BOND : angle 1.62117 ( 4) covalent geometry : bond 0.00532 ( 8330) covalent geometry : angle 0.62084 (11354) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.468 Fit side-chains REVERT: A 332 ILE cc_start: 0.7693 (mm) cc_final: 0.7182 (tt) REVERT: B 195 LYS cc_start: 0.7323 (tttt) cc_final: 0.7081 (tttt) REVERT: C 61 MET cc_start: 0.7294 (tmm) cc_final: 0.6647 (tmm) REVERT: C 68 ARG cc_start: 0.7372 (mtp180) cc_final: 0.6394 (mtp180) REVERT: C 105 TYR cc_start: 0.8437 (t80) cc_final: 0.8233 (t80) REVERT: C 135 VAL cc_start: 0.8142 (t) cc_final: 0.7795 (p) REVERT: C 252 LEU cc_start: 0.8813 (tt) cc_final: 0.8504 (tp) REVERT: C 292 PHE cc_start: 0.7491 (m-10) cc_final: 0.7184 (m-10) REVERT: C 296 VAL cc_start: 0.8460 (t) cc_final: 0.8219 (m) REVERT: E 18 ARG cc_start: 0.6945 (mmm-85) cc_final: 0.6709 (mmm-85) REVERT: E 98 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7298 (ttp-170) REVERT: E 106 SER cc_start: 0.8518 (t) cc_final: 0.8203 (p) REVERT: E 132 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6537 (m) outliers start: 27 outliers final: 25 residues processed: 160 average time/residue: 0.3368 time to fit residues: 72.2250 Evaluate side-chains 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 86 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.141267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124178 restraints weight = 11531.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125038 restraints weight = 8247.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126001 restraints weight = 6838.466| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8333 Z= 0.123 Angle : 0.526 9.737 11358 Z= 0.280 Chirality : 0.042 0.156 1345 Planarity : 0.004 0.044 1424 Dihedral : 5.730 52.976 1230 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.20 % Allowed : 15.85 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.58 (0.27), residues: 1065 helix: 2.31 (0.29), residues: 347 sheet: 1.52 (0.32), residues: 274 loop : -0.29 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE E 200 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 399) hydrogen bonds : angle 4.05978 ( 1125) SS BOND : bond 0.00504 ( 2) SS BOND : angle 1.05871 ( 4) covalent geometry : bond 0.00275 ( 8330) covalent geometry : angle 0.52601 (11354) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.146 Fit side-chains REVERT: A 93 MET cc_start: 0.6299 (tpp) cc_final: 0.5446 (tpt) REVERT: A 332 ILE cc_start: 0.7699 (mm) cc_final: 0.7208 (tt) REVERT: C 68 ARG cc_start: 0.7337 (mtp180) cc_final: 0.6449 (mtp180) REVERT: C 135 VAL cc_start: 0.8155 (t) cc_final: 0.7821 (p) REVERT: C 252 LEU cc_start: 0.8735 (tt) cc_final: 0.8515 (tp) REVERT: C 292 PHE cc_start: 0.7434 (m-10) cc_final: 0.7187 (m-10) REVERT: C 296 VAL cc_start: 0.8348 (t) cc_final: 0.8133 (m) REVERT: E 18 ARG cc_start: 0.6894 (mmm-85) cc_final: 0.6649 (mmm-85) REVERT: E 98 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7204 (ttp-170) REVERT: E 106 SER cc_start: 0.8471 (t) cc_final: 0.8157 (p) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.2501 time to fit residues: 48.8780 Evaluate side-chains 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124891 restraints weight = 11620.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125444 restraints weight = 8493.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126336 restraints weight = 6973.422| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8333 Z= 0.116 Angle : 0.521 9.354 11358 Z= 0.274 Chirality : 0.042 0.150 1345 Planarity : 0.003 0.042 1424 Dihedral : 5.545 52.955 1230 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.32 % Allowed : 16.59 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.71 (0.27), residues: 1065 helix: 2.43 (0.29), residues: 347 sheet: 1.59 (0.32), residues: 274 loop : -0.20 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE C 199 TYR 0.016 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 399) hydrogen bonds : angle 3.92530 ( 1125) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.10350 ( 4) covalent geometry : bond 0.00258 ( 8330) covalent geometry : angle 0.52084 (11354) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.896 Fit side-chains REVERT: A 332 ILE cc_start: 0.7734 (mm) cc_final: 0.7263 (tt) REVERT: B 82 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6488 (t70) REVERT: C 68 ARG cc_start: 0.7259 (mtp180) cc_final: 0.6450 (mtp180) REVERT: C 70 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7163 (mp) REVERT: C 135 VAL cc_start: 0.8132 (t) cc_final: 0.7787 (p) REVERT: C 292 PHE cc_start: 0.7376 (m-10) cc_final: 0.7105 (m-10) REVERT: E 18 ARG cc_start: 0.6858 (mmm-85) cc_final: 0.6606 (mmm-85) REVERT: E 106 SER cc_start: 0.8446 (t) cc_final: 0.8122 (p) REVERT: E 218 MET cc_start: 0.7567 (ttt) cc_final: 0.7334 (ttt) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.2836 time to fit residues: 53.6546 Evaluate side-chains 145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121741 restraints weight = 11795.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123972 restraints weight = 7713.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125398 restraints weight = 5741.395| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8333 Z= 0.185 Angle : 0.589 9.480 11358 Z= 0.311 Chirality : 0.044 0.152 1345 Planarity : 0.004 0.053 1424 Dihedral : 5.859 52.996 1230 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.05 % Allowed : 15.98 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.52 (0.27), residues: 1065 helix: 2.27 (0.29), residues: 347 sheet: 1.45 (0.32), residues: 272 loop : -0.29 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.006 0.002 HIS B 209 PHE 0.020 0.002 PHE C 199 TYR 0.016 0.002 TYR E 178 ARG 0.005 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 399) hydrogen bonds : angle 4.14455 ( 1125) SS BOND : bond 0.00688 ( 2) SS BOND : angle 1.52481 ( 4) covalent geometry : bond 0.00441 ( 8330) covalent geometry : angle 0.58855 (11354) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.926 Fit side-chains REVERT: A 332 ILE cc_start: 0.7706 (mm) cc_final: 0.7288 (tt) REVERT: B 82 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6536 (t70) REVERT: C 68 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6391 (mtp180) REVERT: C 135 VAL cc_start: 0.8124 (t) cc_final: 0.7776 (p) REVERT: C 292 PHE cc_start: 0.7426 (m-10) cc_final: 0.7122 (m-10) REVERT: C 296 VAL cc_start: 0.8366 (t) cc_final: 0.8149 (m) REVERT: E 98 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.7277 (ttp-170) REVERT: E 106 SER cc_start: 0.8466 (t) cc_final: 0.8097 (p) outliers start: 25 outliers final: 21 residues processed: 152 average time/residue: 0.2461 time to fit residues: 52.5501 Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.139992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120733 restraints weight = 11749.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123190 restraints weight = 7538.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124587 restraints weight = 5559.977| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8333 Z= 0.122 Angle : 0.532 9.550 11358 Z= 0.280 Chirality : 0.042 0.151 1345 Planarity : 0.004 0.044 1424 Dihedral : 5.579 52.679 1230 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.44 % Allowed : 16.71 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.65 (0.27), residues: 1065 helix: 2.42 (0.29), residues: 347 sheet: 1.50 (0.32), residues: 273 loop : -0.23 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 399) hydrogen bonds : angle 3.94127 ( 1125) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.03860 ( 4) covalent geometry : bond 0.00273 ( 8330) covalent geometry : angle 0.53143 (11354) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.872 Fit side-chains REVERT: A 332 ILE cc_start: 0.7728 (mm) cc_final: 0.7285 (tt) REVERT: B 82 HIS cc_start: 0.6913 (OUTLIER) cc_final: 0.6568 (t70) REVERT: C 68 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6450 (mtp180) REVERT: C 70 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (mp) REVERT: C 135 VAL cc_start: 0.8124 (t) cc_final: 0.7781 (p) REVERT: C 292 PHE cc_start: 0.7459 (m-10) cc_final: 0.7177 (m-10) REVERT: E 98 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7087 (ptt180) REVERT: E 106 SER cc_start: 0.8451 (t) cc_final: 0.8130 (p) REVERT: E 218 MET cc_start: 0.7465 (ttp) cc_final: 0.7209 (ttt) outliers start: 20 outliers final: 16 residues processed: 145 average time/residue: 0.2253 time to fit residues: 44.5172 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119349 restraints weight = 11845.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121766 restraints weight = 7385.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123629 restraints weight = 5404.010| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8333 Z= 0.135 Angle : 0.543 8.889 11358 Z= 0.286 Chirality : 0.043 0.150 1345 Planarity : 0.004 0.044 1424 Dihedral : 5.589 52.599 1230 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 16.83 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.68 (0.27), residues: 1065 helix: 2.43 (0.29), residues: 347 sheet: 1.57 (0.32), residues: 271 loop : -0.23 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.002 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 399) hydrogen bonds : angle 3.95276 ( 1125) SS BOND : bond 0.00496 ( 2) SS BOND : angle 1.22371 ( 4) covalent geometry : bond 0.00309 ( 8330) covalent geometry : angle 0.54291 (11354) Misc. bond : bond 0.00012 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.33 seconds wall clock time: 64 minutes 40.39 seconds (3880.39 seconds total)