Starting phenix.real_space_refine on Wed Feb 14 01:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dph_27635/02_2024/8dph_27635_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5259 2.51 5 N 1367 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1933 Classifications: {'peptide': 264} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 13 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: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'CLR': 2, 'T4U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.68, per 1000 atoms: 0.57 Number of scatterers: 8182 At special positions: 0 Unit cell: (89.18, 120.12, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1367 7.00 C 5259 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 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: 2046 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 35.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.586A pdb=" N MET A 66 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 5.035A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.581A pdb=" N LEU A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.237A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.588A pdb=" N SER A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.637A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.933A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 212 through 246 removed outlier: 4.410A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix removed outlier: 3.508A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 336 removed outlier: 4.270A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.604A 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: 4.980A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 4.430A 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: 3.862A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 4.061A 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: 3.515A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.535A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) 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: 4.300A 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: 3.575A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Processing helix chain 'C' and resid 6 through 25 removed outlier: 4.142A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 4.516A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.402A 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: 7.432A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY B 40 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 86 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.543A 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: 6.961A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.020A 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: 6.964A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.110A 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: 6.839A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.762A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.337A 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: 6.544A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.201A 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: 6.348A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.538A 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: 6.771A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.673A 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: 3.839A 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: 3.715A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.082A 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: 7.160A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.661A 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 148 361 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: 2.37 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1315 1.31 - 1.44: 2288 1.44 - 1.56: 4667 1.56 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8353 Sorted by residual: bond pdb=" C10 T4U A 501 " pdb="CL12 T4U A 501 " ideal model delta sigma weight residual 1.786 1.515 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 1.546 1.414 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C03 T4U A 501 " pdb=" C10 T4U A 501 " ideal model delta sigma weight residual 1.392 1.276 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.550 1.434 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C09 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.383 1.280 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.60: 117 104.60 - 111.95: 4183 111.95 - 119.30: 2747 119.30 - 126.65: 4218 126.65 - 134.00: 126 Bond angle restraints: 11391 Sorted by residual: angle pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 111.00 127.11 -16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N VAL A 156 " ideal model delta sigma weight residual 122.46 116.74 5.72 1.38e+00 5.25e-01 1.72e+01 angle pdb=" N PRO A 159 " pdb=" CA PRO A 159 " pdb=" C PRO A 159 " ideal model delta sigma weight residual 113.57 118.98 -5.41 1.31e+00 5.83e-01 1.71e+01 angle pdb=" N TRP A 130 " pdb=" CA TRP A 130 " pdb=" C TRP A 130 " ideal model delta sigma weight residual 110.97 106.64 4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" C02 T4U A 501 " pdb=" C09 T4U A 501 " pdb=" C04 T4U A 501 " ideal model delta sigma weight residual 122.34 110.97 11.37 3.00e+00 1.11e-01 1.44e+01 ... (remaining 11386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 4923 33.85 - 67.69: 41 67.69 - 101.54: 4 101.54 - 135.39: 3 135.39 - 169.24: 2 Dihedral angle restraints: 4973 sinusoidal: 1811 harmonic: 3162 Sorted by residual: dihedral pdb=" C09 T4U A 501 " pdb=" C04 T4U A 501 " pdb=" C05 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual 93.19 -76.05 169.24 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C04 T4U A 501 " pdb=" C05 T4U A 501 " pdb=" N13 T4U A 501 " pdb=" C07 T4U A 501 " ideal model delta sinusoidal sigma weight residual -80.44 55.04 -135.48 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C11 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual 66.36 -66.78 133.14 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 4970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1267 0.090 - 0.180: 81 0.180 - 0.270: 3 0.270 - 0.360: 0 0.360 - 0.450: 2 Chirality restraints: 1353 Sorted by residual: chirality pdb=" C08 T4U A 501 " pdb=" C01 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C11 T4U A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CB VAL A 156 " pdb=" CA VAL A 156 " pdb=" CG1 VAL A 156 " pdb=" CG2 VAL A 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1350 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA A 155 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA A 155 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 156 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 T4U A 501 " 0.005 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" C03 T4U A 501 " 0.017 2.00e-02 2.50e+03 pdb=" C04 T4U A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C06 T4U A 501 " 0.009 2.00e-02 2.50e+03 pdb=" C08 T4U A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C09 T4U A 501 " -0.011 2.00e-02 2.50e+03 pdb=" C10 T4U A 501 " 0.019 2.00e-02 2.50e+03 pdb=" C11 T4U A 501 " -0.009 2.00e-02 2.50e+03 pdb="CL12 T4U A 501 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO C 236 " 0.062 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 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 157 2.71 - 3.26: 7648 3.26 - 3.80: 12055 3.80 - 4.35: 15280 4.35 - 4.90: 26850 Nonbonded interactions: 61990 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.162 2.440 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.207 2.440 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.229 2.440 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.260 2.440 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.268 2.520 ... (remaining 61985 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.000 Extract box with map and model: 3.830 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.250 Find NCS groups from input model: 0.260 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.005 0.271 8353 Z= 0.375 Angle : 0.592 16.112 11391 Z= 0.318 Chirality : 0.046 0.450 1353 Planarity : 0.003 0.036 1423 Dihedral : 10.989 169.236 2921 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.73 % Allowed : 1.71 % Favored : 97.56 % 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: 1.66 (0.26), residues: 1065 helix: 2.09 (0.30), residues: 328 sheet: 1.31 (0.30), residues: 293 loop : 0.28 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 130 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE C 199 TYR 0.007 0.001 TYR C 105 ARG 0.003 0.000 ARG B 132 *********************** 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 267 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 261 time to evaluate : 0.905 Fit side-chains REVERT: A 153 TYR cc_start: 0.8228 (t80) cc_final: 0.8000 (t80) REVERT: A 318 PHE cc_start: 0.6966 (m-80) cc_final: 0.6686 (m-80) REVERT: B 136 THR cc_start: 0.8155 (p) cc_final: 0.7913 (t) REVERT: B 216 THR cc_start: 0.7833 (p) cc_final: 0.7551 (p) REVERT: B 219 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6607 (p) REVERT: B 230 ASP cc_start: 0.7256 (m-30) cc_final: 0.7053 (m-30) REVERT: C 48 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7270 (mmt-90) REVERT: C 98 SER cc_start: 0.7962 (p) cc_final: 0.7740 (p) REVERT: C 100 VAL cc_start: 0.8604 (p) cc_final: 0.8315 (t) REVERT: C 150 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8088 (mmt180) REVERT: C 168 LEU cc_start: 0.7997 (tp) cc_final: 0.7757 (tt) REVERT: C 325 MET cc_start: 0.6588 (mtt) cc_final: 0.6323 (mmm) REVERT: C 340 ASN cc_start: 0.7330 (t0) cc_final: 0.6931 (t0) REVERT: E 23 SER cc_start: 0.8307 (m) cc_final: 0.7964 (t) REVERT: E 98 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7387 (ptt180) REVERT: E 185 SER cc_start: 0.7835 (t) cc_final: 0.7606 (p) REVERT: E 190 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7322 (mtm110) outliers start: 6 outliers final: 4 residues processed: 265 average time/residue: 0.2030 time to fit residues: 71.6215 Evaluate side-chains 213 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 244 ASN C 88 ASN C 110 ASN C 119 ASN C 220 GLN C 230 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8353 Z= 0.226 Angle : 0.575 7.764 11391 Z= 0.310 Chirality : 0.044 0.231 1353 Planarity : 0.005 0.051 1423 Dihedral : 10.784 176.876 1302 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.81 % Allowed : 10.01 % Favored : 87.18 % 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: 1.47 (0.26), residues: 1065 helix: 1.66 (0.28), residues: 346 sheet: 1.55 (0.31), residues: 283 loop : 0.09 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 332 HIS 0.006 0.001 HIS B 209 PHE 0.019 0.002 PHE C 199 TYR 0.010 0.001 TYR A 368 ARG 0.006 0.001 ARG C 137 *********************** 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 234 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 0.874 Fit side-chains REVERT: A 153 TYR cc_start: 0.8267 (t80) cc_final: 0.8049 (t80) REVERT: A 318 PHE cc_start: 0.6918 (m-80) cc_final: 0.6674 (m-80) REVERT: B 136 THR cc_start: 0.8276 (p) cc_final: 0.7990 (t) REVERT: B 194 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7895 (ttp-110) REVERT: C 48 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7402 (mmt-90) REVERT: C 98 SER cc_start: 0.8082 (p) cc_final: 0.7607 (t) REVERT: C 200 VAL cc_start: 0.7772 (m) cc_final: 0.7560 (p) REVERT: C 258 ASP cc_start: 0.5825 (t0) cc_final: 0.5199 (t0) REVERT: C 325 MET cc_start: 0.6488 (mtt) cc_final: 0.6183 (mmm) REVERT: C 340 ASN cc_start: 0.7448 (t0) cc_final: 0.7112 (t0) REVERT: E 23 SER cc_start: 0.8207 (m) cc_final: 0.7870 (t) REVERT: E 93 MET cc_start: 0.7435 (tpp) cc_final: 0.6729 (tpp) REVERT: E 103 TYR cc_start: 0.8370 (t80) cc_final: 0.8140 (t80) REVERT: E 185 SER cc_start: 0.7883 (t) cc_final: 0.7608 (p) REVERT: E 190 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7649 (mtm110) outliers start: 23 outliers final: 14 residues processed: 226 average time/residue: 0.2115 time to fit residues: 64.4408 Evaluate side-chains 215 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER 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: 2.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 75 GLN C 88 ASN C 110 ASN C 230 ASN E 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8353 Z= 0.243 Angle : 0.560 7.060 11391 Z= 0.305 Chirality : 0.044 0.218 1353 Planarity : 0.005 0.063 1423 Dihedral : 10.764 176.685 1299 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.03 % Allowed : 11.36 % Favored : 84.62 % 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: 1.26 (0.26), residues: 1065 helix: 1.50 (0.28), residues: 341 sheet: 1.51 (0.31), residues: 294 loop : -0.14 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.006 0.001 HIS B 209 PHE 0.016 0.002 PHE A 328 TYR 0.013 0.001 TYR C 105 ARG 0.003 0.000 ARG C 137 *********************** 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 244 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 0.954 Fit side-chains REVERT: A 146 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6994 (m) REVERT: A 318 PHE cc_start: 0.6876 (m-80) cc_final: 0.6670 (m-80) REVERT: B 136 THR cc_start: 0.8368 (p) cc_final: 0.7999 (t) REVERT: B 194 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7912 (ttp-110) REVERT: C 48 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7332 (mmt-90) REVERT: C 98 SER cc_start: 0.8033 (p) cc_final: 0.7702 (t) REVERT: C 200 VAL cc_start: 0.7889 (m) cc_final: 0.7626 (p) REVERT: C 227 SER cc_start: 0.8191 (m) cc_final: 0.7919 (t) REVERT: C 258 ASP cc_start: 0.5801 (t0) cc_final: 0.5253 (t0) REVERT: E 23 SER cc_start: 0.8249 (m) cc_final: 0.7871 (t) REVERT: E 88 SER cc_start: 0.7390 (OUTLIER) cc_final: 0.7178 (t) REVERT: E 93 MET cc_start: 0.7505 (tpp) cc_final: 0.6618 (ttm) REVERT: E 132 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5372 (t) outliers start: 33 outliers final: 22 residues processed: 227 average time/residue: 0.2106 time to fit residues: 63.5781 Evaluate side-chains 225 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 75 GLN C 110 ASN C 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8353 Z= 0.232 Angle : 0.554 8.426 11391 Z= 0.298 Chirality : 0.044 0.220 1353 Planarity : 0.004 0.065 1423 Dihedral : 10.673 176.261 1298 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.91 % Allowed : 12.94 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1065 helix: 1.33 (0.28), residues: 349 sheet: 1.43 (0.31), residues: 296 loop : -0.33 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.006 0.001 HIS B 209 PHE 0.020 0.002 PHE A 328 TYR 0.015 0.001 TYR A 153 ARG 0.003 0.000 ARG C 137 *********************** 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 236 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 0.966 Fit side-chains REVERT: A 146 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7064 (m) REVERT: A 318 PHE cc_start: 0.6836 (m-80) cc_final: 0.6632 (m-80) REVERT: A 323 MET cc_start: 0.7274 (mmt) cc_final: 0.7067 (mmt) REVERT: B 35 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7559 (mtm180) REVERT: B 194 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7880 (ttp-110) REVERT: C 48 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7384 (mmt-90) REVERT: C 98 SER cc_start: 0.8093 (p) cc_final: 0.7807 (t) REVERT: C 100 VAL cc_start: 0.8604 (p) cc_final: 0.8373 (t) REVERT: C 143 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7890 (m) REVERT: C 200 VAL cc_start: 0.7969 (m) cc_final: 0.7685 (p) REVERT: C 258 ASP cc_start: 0.5857 (t0) cc_final: 0.5291 (t0) REVERT: E 23 SER cc_start: 0.8184 (m) cc_final: 0.7858 (t) REVERT: E 88 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7294 (t) REVERT: E 93 MET cc_start: 0.7490 (tpp) cc_final: 0.6805 (ttm) REVERT: E 132 THR cc_start: 0.5644 (OUTLIER) cc_final: 0.5424 (t) outliers start: 32 outliers final: 22 residues processed: 218 average time/residue: 0.2170 time to fit residues: 62.8719 Evaluate side-chains 225 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 110 ASN C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8353 Z= 0.214 Angle : 0.536 6.900 11391 Z= 0.288 Chirality : 0.043 0.218 1353 Planarity : 0.004 0.059 1423 Dihedral : 10.663 175.952 1298 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.03 % Allowed : 13.68 % Favored : 82.30 % 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: 0.99 (0.26), residues: 1065 helix: 1.24 (0.28), residues: 349 sheet: 1.42 (0.31), residues: 295 loop : -0.35 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 96 HIS 0.004 0.001 HIS B 209 PHE 0.015 0.002 PHE A 328 TYR 0.013 0.001 TYR E 59 ARG 0.002 0.000 ARG C 137 *********************** 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 235 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 146 CYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7028 (m) REVERT: C 48 ARG cc_start: 0.7687 (mmt180) cc_final: 0.7440 (mmt-90) REVERT: C 79 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7943 (mt) REVERT: C 98 SER cc_start: 0.8155 (p) cc_final: 0.7872 (t) REVERT: C 100 VAL cc_start: 0.8582 (p) cc_final: 0.8365 (t) REVERT: C 143 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7898 (m) REVERT: C 200 VAL cc_start: 0.7994 (m) cc_final: 0.7680 (p) REVERT: C 258 ASP cc_start: 0.5916 (t0) cc_final: 0.5371 (t0) REVERT: E 23 SER cc_start: 0.8195 (m) cc_final: 0.7835 (t) REVERT: E 78 THR cc_start: 0.7987 (m) cc_final: 0.7693 (t) REVERT: E 93 MET cc_start: 0.7486 (tpp) cc_final: 0.6813 (ttm) REVERT: E 132 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5436 (t) outliers start: 33 outliers final: 25 residues processed: 219 average time/residue: 0.2041 time to fit residues: 59.7710 Evaluate side-chains 228 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 181 SER 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: 1.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8353 Z= 0.229 Angle : 0.548 6.965 11391 Z= 0.294 Chirality : 0.044 0.229 1353 Planarity : 0.004 0.063 1423 Dihedral : 10.689 176.526 1298 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.79 % Allowed : 15.14 % Favored : 81.07 % 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: 0.89 (0.26), residues: 1065 helix: 1.19 (0.28), residues: 349 sheet: 1.38 (0.31), residues: 290 loop : -0.43 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 96 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE B 74 TYR 0.013 0.001 TYR E 59 ARG 0.007 0.000 ARG B 194 *********************** 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 230 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 146 CYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7076 (m) REVERT: B 48 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7626 (p) REVERT: C 48 ARG cc_start: 0.7675 (mmt180) cc_final: 0.7340 (mmt-90) REVERT: C 79 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7960 (mt) REVERT: C 98 SER cc_start: 0.8203 (p) cc_final: 0.7951 (t) REVERT: C 100 VAL cc_start: 0.8583 (p) cc_final: 0.8335 (t) REVERT: C 200 VAL cc_start: 0.7980 (m) cc_final: 0.7691 (p) REVERT: C 258 ASP cc_start: 0.5943 (t0) cc_final: 0.5386 (t0) REVERT: E 23 SER cc_start: 0.8191 (m) cc_final: 0.7847 (t) REVERT: E 78 THR cc_start: 0.8057 (m) cc_final: 0.7744 (t) REVERT: E 88 SER cc_start: 0.7532 (OUTLIER) cc_final: 0.7274 (t) REVERT: E 93 MET cc_start: 0.7487 (tpp) cc_final: 0.6802 (ttm) REVERT: E 132 THR cc_start: 0.5646 (OUTLIER) cc_final: 0.5435 (t) outliers start: 31 outliers final: 26 residues processed: 216 average time/residue: 0.2140 time to fit residues: 61.5836 Evaluate side-chains 226 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 64 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 110 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8353 Z= 0.227 Angle : 0.544 6.870 11391 Z= 0.292 Chirality : 0.044 0.217 1353 Planarity : 0.004 0.057 1423 Dihedral : 10.705 176.719 1298 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.15 % Allowed : 14.77 % Favored : 81.07 % 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: 1.20 (0.28), residues: 354 sheet: 1.28 (0.31), residues: 291 loop : -0.48 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 96 HIS 0.004 0.001 HIS B 209 PHE 0.018 0.002 PHE A 137 TYR 0.012 0.001 TYR E 59 ARG 0.008 0.000 ARG B 194 *********************** 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 233 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 0.816 Fit side-chains REVERT: A 146 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7165 (m) REVERT: B 48 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7672 (p) REVERT: C 48 ARG cc_start: 0.7674 (mmt180) cc_final: 0.7372 (mmt-90) REVERT: C 98 SER cc_start: 0.8203 (p) cc_final: 0.7975 (t) REVERT: C 100 VAL cc_start: 0.8575 (p) cc_final: 0.8343 (t) REVERT: C 143 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (m) REVERT: C 200 VAL cc_start: 0.8059 (m) cc_final: 0.7753 (p) REVERT: C 258 ASP cc_start: 0.5953 (t0) cc_final: 0.5383 (t0) REVERT: E 20 LEU cc_start: 0.7772 (mt) cc_final: 0.7458 (mt) REVERT: E 23 SER cc_start: 0.8191 (m) cc_final: 0.7860 (t) REVERT: E 78 THR cc_start: 0.7990 (m) cc_final: 0.7677 (t) REVERT: E 88 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.7306 (t) REVERT: E 93 MET cc_start: 0.7492 (tpp) cc_final: 0.6816 (ttm) REVERT: E 132 THR cc_start: 0.5703 (OUTLIER) cc_final: 0.5496 (t) outliers start: 34 outliers final: 26 residues processed: 215 average time/residue: 0.2055 time to fit residues: 58.8747 Evaluate side-chains 226 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN C 75 GLN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8353 Z= 0.168 Angle : 0.517 6.904 11391 Z= 0.276 Chirality : 0.043 0.217 1353 Planarity : 0.004 0.050 1423 Dihedral : 10.595 177.210 1298 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.42 % Allowed : 15.87 % Favored : 80.71 % 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: 1.01 (0.26), residues: 1065 helix: 1.38 (0.29), residues: 343 sheet: 1.34 (0.31), residues: 294 loop : -0.36 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.001 PHE B 74 TYR 0.009 0.001 TYR E 59 ARG 0.008 0.000 ARG B 194 *********************** 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 228 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 0.945 Fit side-chains REVERT: A 146 CYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7043 (m) REVERT: B 48 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7675 (p) REVERT: C 48 ARG cc_start: 0.7679 (mmt180) cc_final: 0.7444 (mmt-90) REVERT: C 61 MET cc_start: 0.7975 (tmm) cc_final: 0.7482 (ppp) REVERT: C 98 SER cc_start: 0.8193 (p) cc_final: 0.7968 (t) REVERT: C 100 VAL cc_start: 0.8548 (p) cc_final: 0.8333 (t) REVERT: C 143 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7931 (m) REVERT: C 258 ASP cc_start: 0.5896 (t0) cc_final: 0.5346 (t0) REVERT: E 23 SER cc_start: 0.8140 (m) cc_final: 0.7811 (t) REVERT: E 78 THR cc_start: 0.7935 (m) cc_final: 0.7605 (t) REVERT: E 88 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.7260 (t) REVERT: E 93 MET cc_start: 0.7495 (tpp) cc_final: 0.6844 (ttm) REVERT: E 132 THR cc_start: 0.5599 (OUTLIER) cc_final: 0.5393 (t) outliers start: 28 outliers final: 20 residues processed: 214 average time/residue: 0.2105 time to fit residues: 60.5022 Evaluate side-chains 218 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 132 THR 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: 0.0570 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 110 ASN C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8353 Z= 0.199 Angle : 0.538 7.073 11391 Z= 0.286 Chirality : 0.043 0.230 1353 Planarity : 0.004 0.056 1423 Dihedral : 10.602 177.024 1297 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.54 % Allowed : 16.24 % Favored : 80.22 % 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: 0.89 (0.26), residues: 1065 helix: 1.28 (0.28), residues: 353 sheet: 1.35 (0.31), residues: 289 loop : -0.52 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 324 HIS 0.003 0.001 HIS B 209 PHE 0.017 0.002 PHE A 328 TYR 0.020 0.001 TYR A 153 ARG 0.008 0.000 ARG B 194 *********************** 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 225 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 146 CYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7065 (m) REVERT: B 48 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7692 (p) REVERT: C 48 ARG cc_start: 0.7619 (mmt180) cc_final: 0.7146 (mmt-90) REVERT: C 61 MET cc_start: 0.7957 (tmm) cc_final: 0.7445 (ppp) REVERT: C 98 SER cc_start: 0.8208 (p) cc_final: 0.7976 (t) REVERT: C 100 VAL cc_start: 0.8583 (p) cc_final: 0.8314 (t) REVERT: C 143 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7939 (m) REVERT: C 200 VAL cc_start: 0.7841 (m) cc_final: 0.7633 (p) REVERT: C 258 ASP cc_start: 0.5900 (t0) cc_final: 0.5326 (t0) REVERT: E 23 SER cc_start: 0.8145 (m) cc_final: 0.7826 (t) REVERT: E 78 THR cc_start: 0.7952 (m) cc_final: 0.7618 (t) REVERT: E 88 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.7283 (t) REVERT: E 93 MET cc_start: 0.7497 (tpp) cc_final: 0.6841 (ttm) REVERT: E 127 VAL cc_start: 0.8616 (t) cc_final: 0.8360 (m) REVERT: E 132 THR cc_start: 0.5636 (OUTLIER) cc_final: 0.5430 (t) outliers start: 29 outliers final: 24 residues processed: 210 average time/residue: 0.2080 time to fit residues: 58.4474 Evaluate side-chains 222 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8353 Z= 0.191 Angle : 0.528 7.192 11391 Z= 0.281 Chirality : 0.043 0.235 1353 Planarity : 0.004 0.052 1423 Dihedral : 10.577 177.164 1297 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.66 % Allowed : 16.48 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1065 helix: 1.44 (0.29), residues: 347 sheet: 1.42 (0.31), residues: 285 loop : -0.46 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 324 HIS 0.003 0.001 HIS B 209 PHE 0.021 0.001 PHE A 328 TYR 0.010 0.001 TYR E 59 ARG 0.008 0.000 ARG B 194 ********************** 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 224 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 0.887 Fit side-chains REVERT: A 146 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7050 (m) REVERT: B 48 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7710 (p) REVERT: C 48 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7420 (mmt-90) REVERT: C 61 MET cc_start: 0.7966 (tmm) cc_final: 0.7441 (ppp) REVERT: C 98 SER cc_start: 0.8203 (p) cc_final: 0.7987 (t) REVERT: C 100 VAL cc_start: 0.8591 (p) cc_final: 0.8339 (t) REVERT: C 143 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7940 (m) REVERT: C 258 ASP cc_start: 0.5871 (t0) cc_final: 0.5279 (t0) REVERT: E 23 SER cc_start: 0.8133 (m) cc_final: 0.7812 (t) REVERT: E 78 THR cc_start: 0.7937 (m) cc_final: 0.7595 (t) REVERT: E 88 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7300 (t) REVERT: E 93 MET cc_start: 0.7496 (tpp) cc_final: 0.6842 (ttm) REVERT: E 127 VAL cc_start: 0.8616 (t) cc_final: 0.8359 (m) REVERT: E 132 THR cc_start: 0.5655 (OUTLIER) cc_final: 0.5449 (t) outliers start: 30 outliers final: 23 residues processed: 209 average time/residue: 0.2078 time to fit residues: 58.0911 Evaluate side-chains 220 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108282 restraints weight = 12594.021| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.96 r_work: 0.3253 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8353 Z= 0.320 Angle : 0.611 7.015 11391 Z= 0.328 Chirality : 0.046 0.246 1353 Planarity : 0.005 0.072 1423 Dihedral : 10.774 176.585 1297 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.66 % Allowed : 16.48 % Favored : 79.85 % 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: 0.66 (0.26), residues: 1065 helix: 1.13 (0.28), residues: 349 sheet: 1.26 (0.31), residues: 290 loop : -0.71 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 324 HIS 0.004 0.001 HIS B 209 PHE 0.029 0.002 PHE C 241 TYR 0.013 0.002 TYR E 59 ARG 0.008 0.001 ARG B 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.04 seconds wall clock time: 41 minutes 15.39 seconds (2475.39 seconds total)