Starting phenix.real_space_refine on Mon Mar 11 12:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/03_2024/8dpg_27634_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/03_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_27634/03_2024/8dpg_27634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/03_2024/8dpg_27634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/03_2024/8dpg_27634_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpg_27634/03_2024/8dpg_27634_trim_updated.pdb" } 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-5265/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: 4.84, per 1000 atoms: 0.59 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: 3.30 Conformation dependent library (CDL) restraints added in 1.5 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... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 35.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.527A pdb=" N MET A 66 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 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 107 through 116 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 157 removed outlier: 4.210A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 185 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 195 removed outlier: 3.928A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 212 through 246 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) removed outlier: 5.123A pdb=" N ILE A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 336 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 343 through 361 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) removed outlier: 4.370A pdb=" N SER A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'B' and resid 7 through 32 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) removed outlier: 4.004A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.590A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.682A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 186 through 203 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 242 removed outlier: 3.515A pdb=" N ILE B 227 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 25 removed outlier: 4.059A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 4.589A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.414A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLY B 40 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N VAL B 86 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) 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= C, 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: 3.774A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'C' and resid 190 through 192 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= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.801A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (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= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.432A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (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= H, 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) Processing sheet with id= I, 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= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.664A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 7.268A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 removed outlier: 3.521A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 900 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: 2.38 Time building geometry restraints manager: 3.37 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: 133 2.70 - 3.25: 7556 3.25 - 3.80: 11951 3.80 - 4.35: 15506 4.35 - 4.90: 27102 Nonbonded interactions: 62248 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 62243 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: 1.050 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: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.240 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- 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= 0.152 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 : 0.887 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: 0.2043 time to fit residues: 50.1263 Evaluate side-chains 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.6736 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8330 Z= 0.208 Angle : 0.530 6.874 11354 Z= 0.286 Chirality : 0.043 0.142 1345 Planarity : 0.004 0.038 1424 Dihedral : 6.722 79.189 1231 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.07 % Allowed : 8.66 % Favored : 89.27 % 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: 1.60 (0.26), residues: 1065 helix: 1.68 (0.29), residues: 347 sheet: 1.50 (0.30), residues: 285 loop : 0.35 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 102 ARG 0.004 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 155 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.889 Fit side-chains REVERT: C 61 MET cc_start: 0.7447 (tmm) cc_final: 0.6897 (tmm) REVERT: C 68 ARG cc_start: 0.7575 (mtp180) cc_final: 0.6406 (mtp180) REVERT: C 135 VAL cc_start: 0.8020 (t) cc_final: 0.7818 (p) REVERT: C 252 LEU cc_start: 0.8445 (tp) cc_final: 0.8094 (tt) REVERT: C 292 PHE cc_start: 0.7661 (m-10) cc_final: 0.7290 (m-10) REVERT: C 303 ASP cc_start: 0.7221 (t0) cc_final: 0.6955 (m-30) REVERT: C 334 SER cc_start: 0.8096 (m) cc_final: 0.7709 (p) REVERT: E 98 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7211 (ttt180) REVERT: E 106 SER cc_start: 0.8516 (t) cc_final: 0.8125 (p) REVERT: E 115 THR cc_start: 0.6764 (p) cc_final: 0.6371 (t) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.2167 time to fit residues: 42.1529 Evaluate side-chains 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 307 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 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 220 GLN C 230 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8330 Z= 0.226 Angle : 0.533 9.586 11354 Z= 0.284 Chirality : 0.043 0.137 1345 Planarity : 0.004 0.036 1424 Dihedral : 6.390 59.773 1230 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.05 % Allowed : 9.63 % Favored : 87.32 % 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: 1.34 (0.26), residues: 1065 helix: 1.54 (0.29), residues: 351 sheet: 1.36 (0.30), residues: 279 loop : 0.12 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.007 0.002 HIS B 209 PHE 0.017 0.002 PHE C 199 TYR 0.016 0.002 TYR E 59 ARG 0.009 0.001 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 163 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.854 Fit side-chains REVERT: A 80 MET cc_start: 0.6352 (tmm) cc_final: 0.6033 (tmm) REVERT: A 350 LEU cc_start: 0.7176 (tt) cc_final: 0.6925 (mt) REVERT: C 61 MET cc_start: 0.7445 (tmm) cc_final: 0.6891 (tmm) REVERT: C 68 ARG cc_start: 0.7568 (mtp180) cc_final: 0.6389 (mtp180) REVERT: C 135 VAL cc_start: 0.8060 (t) cc_final: 0.7857 (p) REVERT: C 252 LEU cc_start: 0.8417 (tp) cc_final: 0.8171 (tt) REVERT: C 255 LEU cc_start: 0.7336 (mt) cc_final: 0.6899 (mp) REVERT: C 292 PHE cc_start: 0.7698 (m-10) cc_final: 0.7242 (m-10) REVERT: C 296 VAL cc_start: 0.8348 (t) cc_final: 0.8101 (m) REVERT: E 98 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7360 (ptt180) REVERT: E 106 SER cc_start: 0.8551 (t) cc_final: 0.8182 (p) REVERT: E 115 THR cc_start: 0.6964 (p) cc_final: 0.6613 (t) outliers start: 25 outliers final: 15 residues processed: 153 average time/residue: 0.2085 time to fit residues: 42.7998 Evaluate side-chains 149 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 352 VAL Chi-restraints excluded: chain B residue 79 VAL 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 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 C residue 336 LEU Chi-restraints excluded: chain E residue 146 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: 6.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8330 Z= 0.404 Angle : 0.646 7.696 11354 Z= 0.347 Chirality : 0.048 0.250 1345 Planarity : 0.005 0.055 1424 Dihedral : 6.572 65.708 1230 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.17 % Allowed : 13.54 % Favored : 83.29 % 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: 0.70 (0.26), residues: 1065 helix: 1.04 (0.29), residues: 349 sheet: 1.11 (0.31), residues: 275 loop : -0.36 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 211 HIS 0.010 0.003 HIS B 209 PHE 0.029 0.003 PHE A 317 TYR 0.025 0.003 TYR E 59 ARG 0.006 0.001 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 166 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.298 Fit side-chains REVERT: A 80 MET cc_start: 0.6361 (tmm) cc_final: 0.6160 (tmm) REVERT: A 93 MET cc_start: 0.6448 (tpp) cc_final: 0.5680 (tpt) REVERT: C 61 MET cc_start: 0.7399 (tmm) cc_final: 0.6619 (tmm) REVERT: C 68 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6294 (mtp180) REVERT: C 105 TYR cc_start: 0.8410 (t80) cc_final: 0.8203 (t80) REVERT: C 135 VAL cc_start: 0.8043 (t) cc_final: 0.7822 (p) REVERT: C 255 LEU cc_start: 0.7207 (mt) cc_final: 0.6913 (mp) REVERT: C 262 MET cc_start: 0.8271 (mpp) cc_final: 0.7902 (mpp) REVERT: C 292 PHE cc_start: 0.7733 (m-10) cc_final: 0.7416 (m-10) REVERT: C 296 VAL cc_start: 0.8436 (t) cc_final: 0.8163 (m) REVERT: E 18 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6715 (mmm-85) REVERT: E 98 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7047 (ttt180) REVERT: E 106 SER cc_start: 0.8538 (t) cc_final: 0.8181 (p) REVERT: E 132 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6568 (m) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.2231 time to fit residues: 46.4473 Evaluate side-chains 155 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 20 ASP 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 132 ARG 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 146 LEU Chi-restraints excluded: chain C residue 234 PHE 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 208 GLU 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 86 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.6830 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8330 Z= 0.180 Angle : 0.504 6.791 11354 Z= 0.270 Chirality : 0.042 0.134 1345 Planarity : 0.004 0.044 1424 Dihedral : 5.781 53.750 1230 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.07 % Allowed : 15.37 % Favored : 82.56 % 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: 0.85 (0.26), residues: 1065 helix: 1.10 (0.29), residues: 356 sheet: 1.27 (0.31), residues: 280 loop : -0.30 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.001 PHE E 200 TYR 0.012 0.001 TYR E 102 ARG 0.005 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 143 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.826 Fit side-chains REVERT: A 350 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 61 MET cc_start: 0.7426 (tmm) cc_final: 0.7053 (tmm) REVERT: C 68 ARG cc_start: 0.7570 (mtp180) cc_final: 0.6346 (mtp180) REVERT: C 105 TYR cc_start: 0.8404 (t80) cc_final: 0.8201 (t80) REVERT: C 255 LEU cc_start: 0.7344 (mt) cc_final: 0.6865 (mp) REVERT: C 292 PHE cc_start: 0.7717 (m-10) cc_final: 0.7375 (m-10) REVERT: C 296 VAL cc_start: 0.8366 (t) cc_final: 0.8129 (m) REVERT: E 98 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7227 (ptt180) REVERT: E 106 SER cc_start: 0.8450 (t) cc_final: 0.8085 (p) outliers start: 17 outliers final: 12 residues processed: 138 average time/residue: 0.2200 time to fit residues: 40.3872 Evaluate side-chains 137 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 72 THR 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 B residue 219 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 329 THR 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: 0.9990 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 48 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.6823 moved from start: 0.3662 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= 0.169 Angle : 0.491 8.597 11354 Z= 0.262 Chirality : 0.042 0.131 1345 Planarity : 0.004 0.038 1424 Dihedral : 5.539 53.840 1230 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 15.24 % 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: 0.95 (0.26), residues: 1065 helix: 1.19 (0.29), residues: 353 sheet: 1.25 (0.30), residues: 287 loop : -0.21 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.010 0.001 TYR E 102 ARG 0.007 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 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.906 Fit side-chains REVERT: A 350 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6682 (tt) REVERT: C 61 MET cc_start: 0.7475 (tmm) cc_final: 0.7160 (tmm) REVERT: C 68 ARG cc_start: 0.7559 (mtp180) cc_final: 0.6398 (mtp180) REVERT: C 105 TYR cc_start: 0.8390 (t80) cc_final: 0.8111 (t80) REVERT: C 255 LEU cc_start: 0.7336 (mt) cc_final: 0.6898 (mp) REVERT: C 292 PHE cc_start: 0.7690 (m-10) cc_final: 0.7306 (m-10) REVERT: C 296 VAL cc_start: 0.8315 (t) cc_final: 0.8092 (m) REVERT: E 98 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7235 (ptt180) REVERT: E 106 SER cc_start: 0.8443 (t) cc_final: 0.8039 (p) REVERT: E 218 MET cc_start: 0.7471 (ttt) cc_final: 0.7191 (ttt) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.2219 time to fit residues: 38.8145 Evaluate side-chains 136 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 72 THR 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 B residue 219 VAL Chi-restraints excluded: chain C residue 118 ASP 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 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: 0.6980 chunk 11 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 331 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8330 Z= 0.257 Angle : 0.539 8.735 11354 Z= 0.287 Chirality : 0.043 0.142 1345 Planarity : 0.004 0.045 1424 Dihedral : 5.744 53.901 1230 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.56 % Allowed : 15.61 % 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: 0.78 (0.26), residues: 1065 helix: 1.04 (0.29), residues: 359 sheet: 1.14 (0.30), residues: 287 loop : -0.31 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 211 HIS 0.005 0.001 HIS B 209 PHE 0.019 0.002 PHE C 199 TYR 0.014 0.002 TYR E 95 ARG 0.007 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 143 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.773 Fit side-chains REVERT: A 350 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6591 (tt) REVERT: C 68 ARG cc_start: 0.7590 (mtp180) cc_final: 0.6409 (mtp180) REVERT: C 255 LEU cc_start: 0.7313 (mt) cc_final: 0.6903 (mp) REVERT: C 292 PHE cc_start: 0.7715 (m-10) cc_final: 0.7284 (m-10) REVERT: C 296 VAL cc_start: 0.8352 (t) cc_final: 0.8108 (m) REVERT: E 98 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7101 (ptt180) REVERT: E 106 SER cc_start: 0.8448 (t) cc_final: 0.8039 (p) outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 0.2203 time to fit residues: 39.4048 Evaluate side-chains 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 72 THR 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 B residue 219 VAL 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 329 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR 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: 0.1980 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3992 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= 0.167 Angle : 0.489 7.915 11354 Z= 0.260 Chirality : 0.041 0.149 1345 Planarity : 0.004 0.039 1424 Dihedral : 5.484 53.374 1230 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.93 % Allowed : 15.49 % Favored : 81.59 % 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: 0.84 (0.26), residues: 1065 helix: 1.16 (0.29), residues: 359 sheet: 1.16 (0.30), residues: 287 loop : -0.33 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE C 199 TYR 0.009 0.001 TYR E 102 ARG 0.007 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 149 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.923 Fit side-chains REVERT: A 332 ILE cc_start: 0.7533 (mm) cc_final: 0.6977 (tt) REVERT: A 350 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6563 (tt) REVERT: C 68 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6418 (mtp180) REVERT: C 105 TYR cc_start: 0.8392 (t80) cc_final: 0.8153 (t80) REVERT: C 255 LEU cc_start: 0.7298 (mt) cc_final: 0.6873 (mp) REVERT: C 292 PHE cc_start: 0.7690 (m-10) cc_final: 0.7288 (m-10) REVERT: C 296 VAL cc_start: 0.8317 (t) cc_final: 0.8084 (m) REVERT: E 18 ARG cc_start: 0.6673 (mmm-85) cc_final: 0.6471 (mmm-85) REVERT: E 98 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7181 (ptt180) REVERT: E 106 SER cc_start: 0.8412 (t) cc_final: 0.8003 (p) REVERT: E 218 MET cc_start: 0.7464 (ttt) cc_final: 0.7081 (ttt) outliers start: 24 outliers final: 19 residues processed: 140 average time/residue: 0.2192 time to fit residues: 41.1559 Evaluate side-chains 144 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 350 LEU 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 132 ARG 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 74 SER Chi-restraints excluded: chain C residue 118 ASP 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 160 THR 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: 10.0000 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8330 Z= 0.308 Angle : 0.578 8.459 11354 Z= 0.305 Chirality : 0.045 0.166 1345 Planarity : 0.004 0.048 1424 Dihedral : 5.897 53.406 1230 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.17 % Allowed : 15.85 % 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: 0.56 (0.26), residues: 1065 helix: 0.97 (0.29), residues: 359 sheet: 0.94 (0.30), residues: 293 loop : -0.50 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 36 HIS 0.006 0.002 HIS B 209 PHE 0.021 0.002 PHE C 199 TYR 0.016 0.002 TYR E 95 ARG 0.007 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 152 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.820 Fit side-chains REVERT: A 332 ILE cc_start: 0.7574 (mm) cc_final: 0.7020 (tt) REVERT: A 350 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6615 (tt) REVERT: C 68 ARG cc_start: 0.7597 (mtp180) cc_final: 0.6401 (mtp180) REVERT: C 105 TYR cc_start: 0.8391 (t80) cc_final: 0.8180 (t80) REVERT: C 255 LEU cc_start: 0.7342 (mt) cc_final: 0.6964 (mp) REVERT: C 292 PHE cc_start: 0.7709 (m-10) cc_final: 0.7258 (m-10) REVERT: C 296 VAL cc_start: 0.8394 (t) cc_final: 0.8135 (m) REVERT: E 98 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.7082 (ptt180) REVERT: E 106 SER cc_start: 0.8422 (t) cc_final: 0.8022 (p) outliers start: 26 outliers final: 22 residues processed: 142 average time/residue: 0.2033 time to fit residues: 39.1699 Evaluate side-chains 147 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 155 ASN 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 146 SER Chi-restraints excluded: chain E residue 160 THR 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: 0.1980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8330 Z= 0.151 Angle : 0.493 6.691 11354 Z= 0.262 Chirality : 0.042 0.132 1345 Planarity : 0.004 0.038 1424 Dihedral : 5.547 53.002 1230 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.20 % Allowed : 16.46 % Favored : 81.34 % 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: 0.73 (0.26), residues: 1065 helix: 1.13 (0.29), residues: 359 sheet: 1.05 (0.30), residues: 288 loop : -0.42 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE E 200 TYR 0.008 0.001 TYR E 102 ARG 0.008 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 140 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.849 Fit side-chains REVERT: A 332 ILE cc_start: 0.7572 (mm) cc_final: 0.7037 (tt) REVERT: C 68 ARG cc_start: 0.7573 (mtp180) cc_final: 0.6439 (mtp180) REVERT: C 255 LEU cc_start: 0.7372 (mt) cc_final: 0.6945 (mp) REVERT: C 292 PHE cc_start: 0.7668 (m-10) cc_final: 0.7217 (m-10) REVERT: E 98 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7171 (ptt180) REVERT: E 106 SER cc_start: 0.8390 (t) cc_final: 0.7984 (p) REVERT: E 218 MET cc_start: 0.7175 (ttp) cc_final: 0.6539 (ttt) REVERT: E 227 PHE cc_start: 0.7938 (m-10) cc_final: 0.7499 (m-10) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.2226 time to fit residues: 39.1080 Evaluate side-chains 137 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 ILE 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 132 ARG Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 160 THR 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: 0.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121537 restraints weight = 11534.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123852 restraints weight = 7651.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125460 restraints weight = 5700.454| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8330 Z= 0.236 Angle : 0.523 6.969 11354 Z= 0.277 Chirality : 0.043 0.143 1345 Planarity : 0.004 0.042 1424 Dihedral : 5.671 53.184 1230 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.07 % Allowed : 17.07 % 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: 0.68 (0.26), residues: 1065 helix: 1.11 (0.29), residues: 359 sheet: 1.00 (0.31), residues: 287 loop : -0.45 (0.30), residues: 419 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 0.016 0.002 PHE C 199 TYR 0.012 0.002 TYR E 95 ARG 0.006 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.43 seconds wall clock time: 35 minutes 14.31 seconds (2114.31 seconds total)