Starting phenix.real_space_refine on Fri Jul 19 15:51:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_27634_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_27634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_27634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_27634_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/07_2024/8dpg_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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.91, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.7 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: 1.02 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: 2.29 Time building geometry restraints manager: 3.35 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: 98.99 - 106.42: 198 106.42 - 113.85: 4733 113.85 - 121.28: 4173 121.28 - 128.70: 2183 128.70 - 136.13: 67 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 2.440 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.201 2.440 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.221 2.440 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.264 2.520 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.264 2.440 ... (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 ========== 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: 1.170 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- 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 : 0.002 0.058 8330 Z= 0.144 Angle : 0.487 11.489 11354 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 0.969 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: 0.1987 time to fit residues: 48.7090 Evaluate side-chains 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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: 0.3980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 220 GLN C 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8330 Z= 0.178 Angle : 0.530 7.040 11354 Z= 0.283 Chirality : 0.043 0.137 1345 Planarity : 0.004 0.037 1424 Dihedral : 6.633 76.505 1231 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.56 % Allowed : 7.44 % Favored : 90.00 % 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: 1.95 (0.26), residues: 1065 helix: 2.34 (0.30), residues: 347 sheet: 1.61 (0.30), residues: 279 loop : 0.28 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 130 HIS 0.006 0.001 HIS B 209 PHE 0.013 0.002 PHE B 100 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 *********************** 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 164 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.915 Fit side-chains REVERT: C 61 MET cc_start: 0.7595 (tmm) cc_final: 0.6968 (tmm) REVERT: C 68 ARG cc_start: 0.7581 (mtp180) cc_final: 0.6566 (mtp180) REVERT: C 130 GLU cc_start: 0.7121 (mp0) cc_final: 0.6705 (mp0) REVERT: C 135 VAL cc_start: 0.8016 (t) cc_final: 0.7777 (p) REVERT: C 292 PHE cc_start: 0.7638 (m-10) cc_final: 0.7283 (m-80) REVERT: C 303 ASP cc_start: 0.7177 (t0) cc_final: 0.6881 (m-30) REVERT: C 334 SER cc_start: 0.8080 (m) cc_final: 0.7731 (p) REVERT: E 98 ARG cc_start: 0.7617 (ttp-170) cc_final: 0.6906 (ttt180) REVERT: E 106 SER cc_start: 0.8499 (t) cc_final: 0.8080 (p) outliers start: 21 outliers final: 10 residues processed: 153 average time/residue: 0.2113 time to fit residues: 44.9439 Evaluate side-chains 149 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 198 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 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN C 230 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8330 Z= 0.204 Angle : 0.526 8.936 11354 Z= 0.279 Chirality : 0.043 0.138 1345 Planarity : 0.004 0.037 1424 Dihedral : 6.285 58.415 1230 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.07 % Allowed : 11.10 % Favored : 86.83 % 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: 1.91 (0.26), residues: 1065 helix: 2.49 (0.29), residues: 343 sheet: 1.54 (0.31), residues: 274 loop : 0.16 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.006 0.001 HIS B 209 PHE 0.016 0.002 PHE C 199 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** 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 157 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.866 Fit side-chains REVERT: B 110 VAL cc_start: 0.7872 (t) cc_final: 0.7445 (m) REVERT: C 61 MET cc_start: 0.7550 (tmm) cc_final: 0.7034 (tmm) REVERT: C 68 ARG cc_start: 0.7514 (mtp180) cc_final: 0.6401 (mtp180) REVERT: C 135 VAL cc_start: 0.8060 (t) cc_final: 0.7768 (p) REVERT: C 252 LEU cc_start: 0.8423 (tp) cc_final: 0.8151 (tt) REVERT: C 255 LEU cc_start: 0.7323 (mt) cc_final: 0.6913 (mp) REVERT: C 292 PHE cc_start: 0.7689 (m-10) cc_final: 0.7260 (m-10) REVERT: C 298 ASP cc_start: 0.7871 (t70) cc_final: 0.7651 (t0) REVERT: C 303 ASP cc_start: 0.7281 (t0) cc_final: 0.7077 (m-30) REVERT: C 334 SER cc_start: 0.8108 (m) cc_final: 0.7773 (p) REVERT: E 98 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.6946 (ptt180) REVERT: E 106 SER cc_start: 0.8525 (t) cc_final: 0.8153 (p) REVERT: E 115 THR cc_start: 0.6832 (p) cc_final: 0.6447 (t) REVERT: E 181 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (m) outliers start: 17 outliers final: 11 residues processed: 152 average time/residue: 0.2158 time to fit residues: 44.6910 Evaluate side-chains 151 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 103 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 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 E residue 181 SER 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 97 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 98 optimal weight: 0.0010 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.0020 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 overall best weight: 0.2806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8330 Z= 0.125 Angle : 0.481 8.487 11354 Z= 0.253 Chirality : 0.041 0.165 1345 Planarity : 0.003 0.034 1424 Dihedral : 5.853 59.602 1230 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 13.41 % Favored : 84.76 % 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: 2.00 (0.27), residues: 1065 helix: 2.59 (0.29), residues: 346 sheet: 1.60 (0.31), residues: 275 loop : 0.17 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.003 0.001 HIS B 209 PHE 0.010 0.001 PHE C 199 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 *********************** 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 150 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.799 Fit side-chains REVERT: B 110 VAL cc_start: 0.7839 (t) cc_final: 0.7436 (m) REVERT: C 61 MET cc_start: 0.7610 (tmm) cc_final: 0.7227 (tmm) REVERT: C 68 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6347 (mtp180) REVERT: C 135 VAL cc_start: 0.8139 (t) cc_final: 0.7794 (p) REVERT: C 252 LEU cc_start: 0.8329 (tp) cc_final: 0.8046 (tt) REVERT: C 255 LEU cc_start: 0.7393 (mt) cc_final: 0.7011 (mp) REVERT: C 292 PHE cc_start: 0.7648 (m-10) cc_final: 0.7198 (m-80) REVERT: C 298 ASP cc_start: 0.7836 (t70) cc_final: 0.7609 (t0) REVERT: C 303 ASP cc_start: 0.7248 (t0) cc_final: 0.6932 (m-30) REVERT: C 334 SER cc_start: 0.8054 (m) cc_final: 0.7718 (p) REVERT: E 98 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7024 (ttt180) REVERT: E 106 SER cc_start: 0.8496 (t) cc_final: 0.8091 (p) REVERT: E 115 THR cc_start: 0.6901 (p) cc_final: 0.6513 (t) REVERT: E 227 PHE cc_start: 0.8252 (m-10) cc_final: 0.8036 (m-10) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.2168 time to fit residues: 42.7133 Evaluate side-chains 139 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 166 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8330 Z= 0.223 Angle : 0.531 9.383 11354 Z= 0.283 Chirality : 0.043 0.141 1345 Planarity : 0.004 0.039 1424 Dihedral : 5.849 55.443 1230 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 13.66 % Favored : 83.78 % 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: 1.76 (0.26), residues: 1065 helix: 2.35 (0.29), residues: 353 sheet: 1.48 (0.31), residues: 274 loop : 0.00 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 211 HIS 0.006 0.001 HIS B 209 PHE 0.019 0.002 PHE C 199 TYR 0.017 0.002 TYR E 178 ARG 0.007 0.000 ARG E 18 *********************** 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 158 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.785 Fit side-chains REVERT: A 332 ILE cc_start: 0.7509 (mm) cc_final: 0.6931 (tt) REVERT: C 61 MET cc_start: 0.7598 (tmm) cc_final: 0.7138 (tmm) REVERT: C 68 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6260 (mtp180) REVERT: C 135 VAL cc_start: 0.8141 (t) cc_final: 0.7769 (p) REVERT: C 252 LEU cc_start: 0.8374 (tp) cc_final: 0.8121 (tt) REVERT: C 255 LEU cc_start: 0.7384 (mt) cc_final: 0.6976 (mp) REVERT: C 262 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: C 292 PHE cc_start: 0.7664 (m-10) cc_final: 0.7201 (m-10) REVERT: C 298 ASP cc_start: 0.7838 (t70) cc_final: 0.7637 (t0) REVERT: C 303 ASP cc_start: 0.7357 (t0) cc_final: 0.7125 (m-30) REVERT: E 18 ARG cc_start: 0.6693 (mmm-85) cc_final: 0.6493 (mmm-85) REVERT: E 98 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.6893 (ttt180) REVERT: E 106 SER cc_start: 0.8528 (t) cc_final: 0.8137 (p) REVERT: E 115 THR cc_start: 0.7001 (p) cc_final: 0.6609 (t) REVERT: E 132 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6320 (m) outliers start: 21 outliers final: 17 residues processed: 150 average time/residue: 0.2044 time to fit residues: 41.3951 Evaluate side-chains 152 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 72 THR 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 100 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU 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 35 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8330 Z= 0.169 Angle : 0.488 9.099 11354 Z= 0.260 Chirality : 0.042 0.136 1345 Planarity : 0.003 0.036 1424 Dihedral : 5.566 54.116 1230 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.32 % Allowed : 14.63 % Favored : 83.05 % 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: 2.45 (0.29), residues: 353 sheet: 1.53 (0.31), residues: 274 loop : -0.01 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG E 18 *********************** 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 148 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.900 Fit side-chains REVERT: A 93 MET cc_start: 0.6263 (tpt) cc_final: 0.5844 (tpt) REVERT: A 332 ILE cc_start: 0.7537 (mm) cc_final: 0.6978 (tt) REVERT: B 194 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7165 (mtp-110) REVERT: C 61 MET cc_start: 0.7615 (tmm) cc_final: 0.7329 (tmm) REVERT: C 68 ARG cc_start: 0.7505 (mtp180) cc_final: 0.6280 (mtp180) REVERT: C 135 VAL cc_start: 0.8136 (t) cc_final: 0.7759 (p) REVERT: C 252 LEU cc_start: 0.8346 (tp) cc_final: 0.8104 (tt) REVERT: C 255 LEU cc_start: 0.7381 (mt) cc_final: 0.6916 (mp) REVERT: C 292 PHE cc_start: 0.7670 (m-10) cc_final: 0.7223 (m-10) REVERT: C 298 ASP cc_start: 0.7801 (t70) cc_final: 0.7597 (t0) REVERT: C 303 ASP cc_start: 0.7323 (t0) cc_final: 0.7121 (m-30) REVERT: E 98 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.6898 (ttt180) REVERT: E 106 SER cc_start: 0.8503 (t) cc_final: 0.8092 (p) outliers start: 19 outliers final: 17 residues processed: 141 average time/residue: 0.2108 time to fit residues: 39.9029 Evaluate side-chains 146 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER 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 79 VAL 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 100 VAL 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 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 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8330 Z= 0.198 Angle : 0.515 9.224 11354 Z= 0.273 Chirality : 0.042 0.138 1345 Planarity : 0.004 0.040 1424 Dihedral : 5.546 54.252 1230 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 15.12 % Favored : 82.32 % 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: 1.78 (0.26), residues: 1065 helix: 2.42 (0.29), residues: 353 sheet: 1.56 (0.31), residues: 274 loop : -0.08 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 E 18 *********************** 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 145 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.026 Fit side-chains REVERT: A 93 MET cc_start: 0.6219 (tpt) cc_final: 0.5806 (tpt) REVERT: A 332 ILE cc_start: 0.7581 (mm) cc_final: 0.7046 (tt) REVERT: B 194 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7166 (mtp-110) REVERT: C 61 MET cc_start: 0.7628 (tmm) cc_final: 0.7362 (tmm) REVERT: C 68 ARG cc_start: 0.7546 (mtp180) cc_final: 0.6364 (mtp180) REVERT: C 135 VAL cc_start: 0.8132 (t) cc_final: 0.7741 (p) REVERT: C 252 LEU cc_start: 0.8363 (tp) cc_final: 0.8110 (tt) REVERT: C 255 LEU cc_start: 0.7297 (mt) cc_final: 0.6854 (mp) REVERT: C 292 PHE cc_start: 0.7706 (m-10) cc_final: 0.7288 (m-80) REVERT: C 303 ASP cc_start: 0.7354 (t0) cc_final: 0.7150 (m-30) REVERT: E 98 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.6868 (ttt180) REVERT: E 106 SER cc_start: 0.8475 (t) cc_final: 0.8098 (p) REVERT: E 132 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6478 (m) outliers start: 21 outliers final: 20 residues processed: 140 average time/residue: 0.2229 time to fit residues: 41.7791 Evaluate side-chains 144 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU 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 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 100 VAL 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 34 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8330 Z= 0.177 Angle : 0.499 8.869 11354 Z= 0.264 Chirality : 0.042 0.139 1345 Planarity : 0.003 0.040 1424 Dihedral : 5.425 53.764 1230 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.44 % Allowed : 15.37 % Favored : 82.20 % 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: 1.81 (0.27), residues: 1065 helix: 2.48 (0.29), residues: 353 sheet: 1.47 (0.31), residues: 279 loop : -0.04 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG E 18 *********************** 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 138 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.976 Fit side-chains REVERT: A 93 MET cc_start: 0.6077 (tpt) cc_final: 0.5676 (tpt) REVERT: A 332 ILE cc_start: 0.7587 (mm) cc_final: 0.7064 (tt) REVERT: B 194 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7122 (mtp-110) REVERT: C 61 MET cc_start: 0.7622 (tmm) cc_final: 0.7396 (tmm) REVERT: C 68 ARG cc_start: 0.7544 (mtp180) cc_final: 0.6408 (mtp180) REVERT: C 135 VAL cc_start: 0.8125 (t) cc_final: 0.7734 (p) REVERT: C 255 LEU cc_start: 0.7325 (mt) cc_final: 0.6885 (mp) REVERT: C 292 PHE cc_start: 0.7679 (m-10) cc_final: 0.7247 (m-80) REVERT: C 303 ASP cc_start: 0.7364 (t0) cc_final: 0.7159 (m-30) REVERT: E 98 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.6854 (ttt180) REVERT: E 106 SER cc_start: 0.8460 (t) cc_final: 0.8073 (p) REVERT: E 132 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6449 (m) REVERT: E 218 MET cc_start: 0.7599 (ttt) cc_final: 0.7278 (ttt) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.2155 time to fit residues: 38.7622 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU 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 132 ARG Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 SER 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 34 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 A 331 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8330 Z= 0.244 Angle : 0.552 8.975 11354 Z= 0.290 Chirality : 0.043 0.140 1345 Planarity : 0.004 0.045 1424 Dihedral : 5.613 53.519 1230 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.80 % Allowed : 15.24 % 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: 1.68 (0.27), residues: 1065 helix: 2.38 (0.29), residues: 354 sheet: 1.42 (0.31), residues: 277 loop : -0.15 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.006 0.001 HIS B 209 PHE 0.019 0.002 PHE C 199 TYR 0.016 0.002 TYR E 178 ARG 0.004 0.000 ARG E 18 *********************** 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 150 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.744 Fit side-chains REVERT: A 93 MET cc_start: 0.6076 (tpt) cc_final: 0.5671 (tpt) REVERT: A 332 ILE cc_start: 0.7586 (mm) cc_final: 0.7064 (tt) REVERT: B 194 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7176 (mtp-110) REVERT: C 61 MET cc_start: 0.7618 (tmm) cc_final: 0.7333 (tmm) REVERT: C 68 ARG cc_start: 0.7531 (mtp180) cc_final: 0.6384 (mtp180) REVERT: C 135 VAL cc_start: 0.8118 (t) cc_final: 0.7728 (p) REVERT: C 255 LEU cc_start: 0.7280 (mt) cc_final: 0.6878 (mp) REVERT: C 292 PHE cc_start: 0.7658 (m-10) cc_final: 0.7220 (m-80) REVERT: E 98 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7294 (ttp-170) REVERT: E 106 SER cc_start: 0.8469 (t) cc_final: 0.8136 (p) outliers start: 23 outliers final: 21 residues processed: 144 average time/residue: 0.2160 time to fit residues: 41.4925 Evaluate side-chains 149 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU 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 132 ARG 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 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 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 102 optimal weight: 0.0270 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.0040 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8330 Z= 0.158 Angle : 0.505 9.192 11354 Z= 0.265 Chirality : 0.042 0.131 1345 Planarity : 0.003 0.042 1424 Dihedral : 5.397 52.842 1230 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.20 % Allowed : 16.10 % Favored : 81.71 % 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: 2.48 (0.29), residues: 353 sheet: 1.45 (0.31), residues: 277 loop : -0.14 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG E 18 ********************** 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 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.762 Fit side-chains REVERT: A 93 MET cc_start: 0.5984 (tpt) cc_final: 0.5457 (tpt) REVERT: A 332 ILE cc_start: 0.7594 (mm) cc_final: 0.7093 (tt) REVERT: B 194 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7204 (mtp-110) REVERT: C 61 MET cc_start: 0.7680 (tmm) cc_final: 0.7159 (tmm) REVERT: C 68 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6502 (mtp180) REVERT: C 135 VAL cc_start: 0.8117 (t) cc_final: 0.7750 (p) REVERT: C 255 LEU cc_start: 0.7355 (mt) cc_final: 0.6899 (mp) REVERT: C 292 PHE cc_start: 0.7692 (m-10) cc_final: 0.7248 (m-80) REVERT: E 18 ARG cc_start: 0.6373 (mmm-85) cc_final: 0.6156 (mmm-85) REVERT: E 98 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7166 (ttp-170) REVERT: E 106 SER cc_start: 0.8451 (t) cc_final: 0.8091 (p) REVERT: E 218 MET cc_start: 0.7572 (ttt) cc_final: 0.7165 (ttt) outliers start: 18 outliers final: 17 residues processed: 131 average time/residue: 0.2199 time to fit residues: 38.2277 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU 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 132 ARG Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 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 = 0.3792 r_free = 0.3792 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124197 restraints weight = 11534.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126383 restraints weight = 7590.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127658 restraints weight = 5711.952| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8330 Z= 0.192 Angle : 0.520 8.590 11354 Z= 0.273 Chirality : 0.042 0.145 1345 Planarity : 0.004 0.045 1424 Dihedral : 5.425 52.719 1230 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.32 % Allowed : 15.85 % Favored : 81.83 % 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: 1.70 (0.27), residues: 1065 helix: 2.46 (0.29), residues: 354 sheet: 1.39 (0.31), residues: 278 loop : -0.17 (0.30), residues: 433 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.30 seconds wall clock time: 34 minutes 18.20 seconds (2058.20 seconds total)