Starting phenix.real_space_refine on Sat Dec 28 10:49:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635.map" model { file = "/net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dph_27635/12_2024/8dph_27635_trim.cif" } 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.39, per 1000 atoms: 0.41 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 38.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.501A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.035A 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 106 through 117 removed outlier: 3.555A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) 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 158 removed outlier: 4.237A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.669A pdb=" N HIS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.714A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) 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 194 removed outlier: 3.933A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 6.954A pdb=" N GLU A 198 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 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) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.508A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.270A 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 342 through 360 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) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.862A 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) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.515A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.515A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.778A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.881A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) 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 243 removed outlier: 3.682A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.559A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.642A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.645A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.543A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.771A 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) removed outlier: 6.779A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.709A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (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=AA4, 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: 6.400A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.839A 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=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.977A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (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=AA7, 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=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.045A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (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=AA9, 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=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.298A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.787A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1092 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: 2.52 Time building geometry restraints manager: 2.50 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 1.757 1.515 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C09 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.408 1.280 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C03 T4U A 501 " pdb=" C10 T4U A 501 " ideal model delta sigma weight residual 1.383 1.276 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 1.508 1.414 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.458 1.517 -0.059 1.29e-02 6.01e+03 2.08e+01 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11251 2.00 - 3.99: 114 3.99 - 5.99: 21 5.99 - 7.98: 2 7.98 - 9.98: 3 Bond angle restraints: 11391 Sorted by residual: 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=" CA TRP A 130 " pdb=" CB TRP A 130 " pdb=" CG TRP A 130 " ideal model delta sigma weight residual 113.60 120.77 -7.17 1.90e+00 2.77e-01 1.43e+01 angle pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 119.19 123.08 -3.89 1.06e+00 8.90e-01 1.35e+01 ... (remaining 11386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4792 17.27 - 34.54: 146 34.54 - 51.80: 32 51.80 - 69.07: 5 69.07 - 86.34: 3 Dihedral angle restraints: 4978 sinusoidal: 1816 harmonic: 3162 Sorted by residual: dihedral pdb=" CA ALA E 131 " pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+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 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 161 " pdb=" CG GLU A 161 " pdb=" CD GLU A 161 " pdb=" OE1 GLU A 161 " ideal model delta sinusoidal sigma weight residual 0.00 86.34 -86.34 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 4975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1264 0.089 - 0.178: 84 0.178 - 0.267: 4 0.267 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 1353 Sorted by residual: 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 chirality pdb=" CA ARG A 157 " pdb=" N ARG A 157 " pdb=" C ARG A 157 " pdb=" CB ARG A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+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: 154 2.71 - 3.26: 7606 3.26 - 3.80: 12043 3.80 - 4.35: 15220 4.35 - 4.90: 26835 Nonbonded interactions: 61858 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.162 3.040 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.207 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.260 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.268 3.120 ... (remaining 61853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.460 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 29.220 ------------------------------------------------------------------------------- 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 0.242 8353 Z= 0.297 Angle : 0.558 9.975 11391 Z= 0.311 Chirality : 0.045 0.446 1353 Planarity : 0.003 0.036 1423 Dihedral : 9.344 86.338 2926 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 to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.960 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: 0.2144 time to fit residues: 75.4267 Evaluate side-chains 213 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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: 0.0670 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 E 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.186 Angle : 0.554 7.816 11391 Z= 0.296 Chirality : 0.043 0.215 1353 Planarity : 0.004 0.044 1423 Dihedral : 5.213 47.842 1307 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.32 % Allowed : 10.13 % Favored : 87.55 % 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: 2.33 (0.29), residues: 338 sheet: 1.54 (0.31), residues: 278 loop : 0.17 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 332 HIS 0.005 0.001 HIS B 209 PHE 0.015 0.002 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.001 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 235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.956 Fit side-chains REVERT: A 153 TYR cc_start: 0.8225 (t80) cc_final: 0.8017 (t80) REVERT: B 136 THR cc_start: 0.8257 (p) cc_final: 0.7990 (t) REVERT: B 194 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7871 (ttp-110) REVERT: C 98 SER cc_start: 0.8047 (p) cc_final: 0.7572 (t) REVERT: C 100 VAL cc_start: 0.8602 (p) cc_final: 0.8376 (t) REVERT: C 150 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.8047 (mmt-90) REVERT: C 258 ASP cc_start: 0.5802 (t0) cc_final: 0.5176 (t0) REVERT: E 23 SER cc_start: 0.8200 (m) cc_final: 0.7843 (t) REVERT: E 103 TYR cc_start: 0.8324 (t80) cc_final: 0.8067 (t80) REVERT: E 185 SER cc_start: 0.7871 (t) cc_final: 0.7622 (p) REVERT: E 190 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7701 (mtm110) outliers start: 19 outliers final: 11 residues processed: 227 average time/residue: 0.2233 time to fit residues: 66.7387 Evaluate side-chains 220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 A residue 181 ILE 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 152 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 88 ASN C 110 ASN C 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.203 Angle : 0.540 7.519 11391 Z= 0.293 Chirality : 0.044 0.221 1353 Planarity : 0.004 0.053 1423 Dihedral : 4.917 40.388 1304 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.42 % Allowed : 10.50 % Favored : 86.08 % 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: 1.69 (0.26), residues: 1065 helix: 2.31 (0.29), residues: 340 sheet: 1.54 (0.30), residues: 286 loop : -0.11 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.006 0.001 HIS B 209 PHE 0.019 0.002 PHE C 241 TYR 0.012 0.001 TYR E 178 ARG 0.008 0.000 ARG C 304 *********************** 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 to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.944 Fit side-chains REVERT: A 146 CYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7016 (m) REVERT: B 136 THR cc_start: 0.8374 (p) cc_final: 0.8040 (t) REVERT: B 194 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7922 (ttp-110) REVERT: C 48 ARG cc_start: 0.7687 (mmt180) cc_final: 0.7366 (mmt-90) REVERT: C 98 SER cc_start: 0.8031 (p) cc_final: 0.7648 (t) REVERT: C 100 VAL cc_start: 0.8639 (p) cc_final: 0.8370 (t) REVERT: C 150 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.8197 (mmt180) REVERT: C 258 ASP cc_start: 0.5783 (t0) cc_final: 0.5188 (t0) REVERT: E 23 SER cc_start: 0.8211 (m) cc_final: 0.7864 (t) REVERT: E 93 MET cc_start: 0.7501 (tpp) cc_final: 0.6604 (ttm) REVERT: E 103 TYR cc_start: 0.8378 (t80) cc_final: 0.8173 (t80) REVERT: E 132 THR cc_start: 0.5564 (OUTLIER) cc_final: 0.5320 (t) REVERT: E 185 SER cc_start: 0.7891 (t) cc_final: 0.7621 (p) REVERT: E 190 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7615 (mtm110) outliers start: 28 outliers final: 22 residues processed: 230 average time/residue: 0.2349 time to fit residues: 70.2960 Evaluate side-chains 232 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 112 LEU 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 B residue 18 MET Chi-restraints excluded: chain B residue 48 THR 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 210 ILE Chi-restraints excluded: chain C residue 147 SER 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 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 78 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: 3.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 119 ASN C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8353 Z= 0.232 Angle : 0.556 7.025 11391 Z= 0.302 Chirality : 0.044 0.219 1353 Planarity : 0.004 0.063 1423 Dihedral : 4.924 38.010 1302 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.66 % Allowed : 12.33 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1065 helix: 2.20 (0.29), residues: 342 sheet: 1.51 (0.30), residues: 284 loop : -0.21 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.006 0.001 HIS B 209 PHE 0.021 0.002 PHE A 328 TYR 0.010 0.001 TYR E 178 ARG 0.005 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 242 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.918 Fit side-chains REVERT: A 63 ILE cc_start: 0.6265 (pt) cc_final: 0.6061 (mm) REVERT: A 146 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7076 (m) REVERT: B 136 THR cc_start: 0.8391 (p) cc_final: 0.7980 (t) REVERT: B 194 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7889 (ttp-110) REVERT: C 48 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7398 (mmt-90) REVERT: C 79 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (mt) REVERT: C 98 SER cc_start: 0.8060 (p) cc_final: 0.7792 (t) REVERT: C 100 VAL cc_start: 0.8615 (p) cc_final: 0.8354 (t) REVERT: C 227 SER cc_start: 0.8165 (m) cc_final: 0.7901 (t) REVERT: C 258 ASP cc_start: 0.5868 (t0) cc_final: 0.5295 (t0) REVERT: E 23 SER cc_start: 0.8216 (m) cc_final: 0.7857 (t) REVERT: E 93 MET cc_start: 0.7542 (tpp) cc_final: 0.6699 (tpp) REVERT: E 132 THR cc_start: 0.5650 (OUTLIER) cc_final: 0.5416 (t) outliers start: 30 outliers final: 21 residues processed: 225 average time/residue: 0.2104 time to fit residues: 62.8589 Evaluate side-chains 232 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS 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 79 LEU 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 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 78 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2883 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= 0.260 Angle : 0.574 7.018 11391 Z= 0.309 Chirality : 0.045 0.218 1353 Planarity : 0.004 0.069 1423 Dihedral : 5.032 38.316 1302 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.42 % Allowed : 13.55 % Favored : 83.03 % 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: 1.49 (0.26), residues: 1065 helix: 2.16 (0.29), residues: 341 sheet: 1.55 (0.31), residues: 284 loop : -0.34 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 63 HIS 0.006 0.001 HIS B 209 PHE 0.015 0.002 PHE C 151 TYR 0.013 0.002 TYR E 59 ARG 0.003 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 237 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 146 CYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7118 (m) REVERT: B 194 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7869 (ttp-110) REVERT: C 48 ARG cc_start: 0.7692 (mmt180) cc_final: 0.7452 (mmt-90) REVERT: C 61 MET cc_start: 0.7660 (ppp) cc_final: 0.7344 (ppp) REVERT: C 79 LEU cc_start: 0.8217 (mp) cc_final: 0.7997 (mt) REVERT: C 98 SER cc_start: 0.8158 (p) cc_final: 0.7880 (t) REVERT: C 100 VAL cc_start: 0.8613 (p) cc_final: 0.8362 (t) REVERT: C 227 SER cc_start: 0.8077 (m) cc_final: 0.7834 (t) REVERT: C 258 ASP cc_start: 0.5993 (t0) cc_final: 0.5434 (t0) REVERT: E 23 SER cc_start: 0.8200 (m) cc_final: 0.7842 (t) REVERT: E 88 SER cc_start: 0.7153 (OUTLIER) cc_final: 0.6923 (t) REVERT: E 132 THR cc_start: 0.5678 (OUTLIER) cc_final: 0.5449 (t) outliers start: 28 outliers final: 20 residues processed: 224 average time/residue: 0.2183 time to fit residues: 64.6802 Evaluate side-chains 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 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 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR 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 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8353 Z= 0.181 Angle : 0.521 6.783 11391 Z= 0.280 Chirality : 0.043 0.216 1353 Planarity : 0.004 0.055 1423 Dihedral : 4.789 38.544 1302 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.81 % Allowed : 15.02 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1065 helix: 2.28 (0.29), residues: 340 sheet: 1.55 (0.31), residues: 281 loop : -0.33 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE B 74 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG C 137 *********************** 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 234 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.871 Fit side-chains REVERT: A 146 CYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7092 (m) REVERT: A 346 MET cc_start: 0.4634 (mmm) cc_final: 0.4312 (mmp) REVERT: C 48 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7433 (mmt-90) REVERT: C 61 MET cc_start: 0.7688 (ppp) cc_final: 0.7192 (ppp) REVERT: C 79 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7949 (mt) REVERT: C 98 SER cc_start: 0.8139 (p) cc_final: 0.7885 (t) REVERT: C 100 VAL cc_start: 0.8595 (p) cc_final: 0.8353 (t) REVERT: C 227 SER cc_start: 0.8027 (m) cc_final: 0.7800 (t) REVERT: C 258 ASP cc_start: 0.5970 (t0) cc_final: 0.5441 (t0) REVERT: E 23 SER cc_start: 0.8129 (m) cc_final: 0.7792 (t) REVERT: E 88 SER cc_start: 0.7025 (OUTLIER) cc_final: 0.6769 (t) REVERT: E 93 MET cc_start: 0.7542 (tpp) cc_final: 0.6845 (ttm) REVERT: E 132 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5370 (t) REVERT: E 179 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7717 (mtt90) outliers start: 23 outliers final: 19 residues processed: 221 average time/residue: 0.2298 time to fit residues: 66.9643 Evaluate side-chains 231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 22 ASN 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 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER 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: 10.0000 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 119 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.196 Angle : 0.533 6.880 11391 Z= 0.286 Chirality : 0.044 0.219 1353 Planarity : 0.004 0.060 1423 Dihedral : 4.788 38.381 1302 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 15.02 % Favored : 81.93 % 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: 1.48 (0.26), residues: 1065 helix: 2.28 (0.28), residues: 342 sheet: 1.52 (0.31), residues: 278 loop : -0.42 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 96 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE B 74 TYR 0.012 0.001 TYR E 59 ARG 0.007 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 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 146 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7102 (m) REVERT: B 48 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (p) REVERT: C 48 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7409 (mmt-90) REVERT: C 61 MET cc_start: 0.7730 (ppp) cc_final: 0.7302 (ppp) REVERT: C 79 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7973 (mt) REVERT: C 98 SER cc_start: 0.8170 (p) cc_final: 0.7935 (t) REVERT: C 100 VAL cc_start: 0.8583 (p) cc_final: 0.8335 (t) REVERT: C 227 SER cc_start: 0.8030 (m) cc_final: 0.7803 (t) REVERT: C 258 ASP cc_start: 0.5993 (t0) cc_final: 0.5457 (t0) REVERT: C 340 ASN cc_start: 0.7298 (t0) cc_final: 0.7040 (t0) REVERT: E 23 SER cc_start: 0.8130 (m) cc_final: 0.7797 (t) REVERT: E 88 SER cc_start: 0.7020 (OUTLIER) cc_final: 0.6768 (t) REVERT: E 93 MET cc_start: 0.7555 (tpp) cc_final: 0.6860 (ttm) outliers start: 25 outliers final: 20 residues processed: 218 average time/residue: 0.2275 time to fit residues: 65.1909 Evaluate side-chains 226 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 238 ILE 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 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.0070 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8353 Z= 0.134 Angle : 0.498 6.757 11391 Z= 0.262 Chirality : 0.042 0.219 1353 Planarity : 0.003 0.043 1423 Dihedral : 4.506 37.926 1302 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.20 % Allowed : 16.12 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1065 helix: 2.50 (0.28), residues: 342 sheet: 1.60 (0.31), residues: 283 loop : -0.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 96 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE B 74 TYR 0.013 0.001 TYR E 178 ARG 0.007 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 220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.895 Fit side-chains REVERT: A 146 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7078 (m) REVERT: C 48 ARG cc_start: 0.7669 (mmt180) cc_final: 0.7436 (mmt-90) REVERT: C 61 MET cc_start: 0.7705 (ppp) cc_final: 0.7035 (ppp) REVERT: C 79 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7870 (mt) REVERT: C 98 SER cc_start: 0.8159 (p) cc_final: 0.7933 (t) REVERT: C 100 VAL cc_start: 0.8534 (p) cc_final: 0.8286 (t) REVERT: C 227 SER cc_start: 0.7957 (m) cc_final: 0.7736 (t) REVERT: C 258 ASP cc_start: 0.5852 (t0) cc_final: 0.5347 (t0) REVERT: C 340 ASN cc_start: 0.7302 (t0) cc_final: 0.7036 (t0) REVERT: E 93 MET cc_start: 0.7549 (tpp) cc_final: 0.6895 (ttm) REVERT: E 127 VAL cc_start: 0.8528 (t) cc_final: 0.8268 (m) REVERT: E 179 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7637 (mtt90) REVERT: E 194 SER cc_start: 0.8474 (p) cc_final: 0.8225 (p) outliers start: 18 outliers final: 13 residues processed: 209 average time/residue: 0.2316 time to fit residues: 63.7307 Evaluate side-chains 213 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 244 ASN C 75 GLN C 88 ASN C 110 ASN C 119 ASN C 155 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8353 Z= 0.178 Angle : 0.524 6.846 11391 Z= 0.277 Chirality : 0.043 0.219 1353 Planarity : 0.004 0.049 1423 Dihedral : 4.473 33.407 1301 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.08 % Allowed : 16.85 % 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: 1.70 (0.26), residues: 1065 helix: 2.55 (0.28), residues: 345 sheet: 1.62 (0.31), residues: 283 loop : -0.39 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 PHE 0.009 0.001 PHE C 199 TYR 0.011 0.001 TYR E 178 ARG 0.007 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 221 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.052 Fit side-chains REVERT: A 146 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7070 (m) REVERT: C 48 ARG cc_start: 0.7664 (mmt180) cc_final: 0.7433 (mmt-90) REVERT: C 61 MET cc_start: 0.7557 (ppp) cc_final: 0.7166 (ppp) REVERT: C 79 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 98 SER cc_start: 0.8172 (p) cc_final: 0.7952 (t) REVERT: C 100 VAL cc_start: 0.8551 (p) cc_final: 0.8290 (t) REVERT: C 227 SER cc_start: 0.8018 (m) cc_final: 0.7795 (t) REVERT: C 258 ASP cc_start: 0.5913 (t0) cc_final: 0.5374 (t0) REVERT: C 340 ASN cc_start: 0.7324 (t0) cc_final: 0.7053 (t0) REVERT: E 23 SER cc_start: 0.8059 (m) cc_final: 0.7734 (t) REVERT: E 93 MET cc_start: 0.7550 (tpp) cc_final: 0.6895 (ttm) REVERT: E 118 THR cc_start: 0.7609 (m) cc_final: 0.7408 (t) REVERT: E 127 VAL cc_start: 0.8541 (t) cc_final: 0.8275 (m) outliers start: 17 outliers final: 14 residues processed: 211 average time/residue: 0.2268 time to fit residues: 62.8686 Evaluate side-chains 220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 208 VAL 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 210 ILE Chi-restraints excluded: chain C residue 79 LEU 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET 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: 0.1980 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 88 ASN C 110 ASN C 119 ASN C 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8353 Z= 0.157 Angle : 0.515 6.988 11391 Z= 0.272 Chirality : 0.043 0.219 1353 Planarity : 0.004 0.048 1423 Dihedral : 4.376 33.133 1301 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 16.85 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1065 helix: 2.63 (0.28), residues: 345 sheet: 1.59 (0.31), residues: 285 loop : -0.36 (0.29), residues: 435 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 0.009 0.001 PHE C 199 TYR 0.013 0.001 TYR E 178 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 223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.815 Fit side-chains REVERT: A 146 CYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7067 (m) REVERT: C 48 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7455 (mmt-90) REVERT: C 79 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7905 (mt) REVERT: C 98 SER cc_start: 0.8181 (p) cc_final: 0.7963 (t) REVERT: C 100 VAL cc_start: 0.8552 (p) cc_final: 0.8280 (t) REVERT: C 227 SER cc_start: 0.8000 (m) cc_final: 0.7768 (t) REVERT: C 258 ASP cc_start: 0.5883 (t0) cc_final: 0.5362 (t0) REVERT: C 340 ASN cc_start: 0.7321 (t0) cc_final: 0.7037 (t0) REVERT: D 51 LEU cc_start: 0.8188 (tp) cc_final: 0.7972 (tt) REVERT: E 23 SER cc_start: 0.8039 (m) cc_final: 0.7720 (t) REVERT: E 93 MET cc_start: 0.7546 (tpp) cc_final: 0.6895 (ttm) REVERT: E 127 VAL cc_start: 0.8530 (t) cc_final: 0.8274 (m) REVERT: E 194 SER cc_start: 0.8449 (p) cc_final: 0.8206 (p) outliers start: 16 outliers final: 14 residues processed: 213 average time/residue: 0.2411 time to fit residues: 68.9488 Evaluate side-chains 221 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 208 VAL 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 210 ILE Chi-restraints excluded: chain C residue 79 LEU 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 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET 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: 0.8980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 88 ASN C 110 ASN C 119 ASN C 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112040 restraints weight = 12631.683| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.98 r_work: 0.3308 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8353 Z= 0.188 Angle : 0.527 6.873 11391 Z= 0.280 Chirality : 0.043 0.218 1353 Planarity : 0.004 0.054 1423 Dihedral : 4.454 33.880 1301 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.95 % Allowed : 17.09 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1065 helix: 2.58 (0.28), residues: 346 sheet: 1.58 (0.31), residues: 280 loop : -0.48 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 324 HIS 0.003 0.001 HIS B 209 PHE 0.014 0.001 PHE A 327 TYR 0.012 0.001 TYR E 178 ARG 0.008 0.000 ARG B 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.25 seconds wall clock time: 41 minutes 24.36 seconds (2484.36 seconds total)