Starting phenix.real_space_refine on Mon Mar 11 18:57:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942_neut_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/8j22_35942/03_2024/8j22_35942_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j22_35942/03_2024/8j22_35942_neut_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= 0.001 sd= 0.022 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 58 5.16 5 Cl 1 4.86 5 C 5654 2.51 5 N 1505 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8856 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1693 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2285 Classifications: {'peptide': 285} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 269} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1805 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'9UJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.58 Number of scatterers: 8856 At special positions: 0 Unit cell: (116.48, 111.28, 123.76, 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 58 16.00 O 1638 8.00 N 1505 7.00 C 5654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 33.8% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.508A pdb=" N ASN A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.575A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 278 removed outlier: 3.607A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.915A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.546A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 37 removed outlier: 3.820A pdb=" N MET C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Proline residue: C 23 - end of helix removed outlier: 3.585A pdb=" N LEU C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 79 through 112 removed outlier: 3.540A pdb=" N ILE C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 123 through 151 removed outlier: 3.607A pdb=" N CYS C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.898A pdb=" N VAL C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 177 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.533A pdb=" N LEU C 181 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 187 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 207 Processing helix chain 'C' and resid 214 through 234 removed outlier: 4.050A pdb=" N LEU C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 248 removed outlier: 4.174A pdb=" N HIS C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 272 removed outlier: 4.480A pdb=" N SER C 256 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 257 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 269 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'D' and resid 2 through 19 Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 removed outlier: 6.861A pdb=" N ALA A 71 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET A 59 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 69 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP A 61 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU A 67 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 72 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS A 87 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 103 removed outlier: 7.011A pdb=" N GLY A 113 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS A 101 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 111 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR A 103 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR A 109 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 114 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 137 " --> pdb=" O CYS A 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 135 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN A 123 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 133 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 144 through 149 removed outlier: 6.972A pdb=" N SER A 158 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS A 147 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 156 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE A 149 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLN A 154 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 155 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 159 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP A 168 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 174 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.184A pdb=" N GLY A 200 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A 188 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 198 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 190 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU A 196 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 218 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A 210 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS A 216 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 227 through 232 removed outlier: 7.112A pdb=" N GLY A 242 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 230 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 240 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 232 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA A 238 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 243 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 260 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 252 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU A 258 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.739A pdb=" N GLY A 304 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 296 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 302 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 44 through 50 removed outlier: 6.788A pdb=" N ILE A 336 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 48 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 334 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 329 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.488A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.537A pdb=" N THR F 118 " --> pdb=" O VAL F 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 92 through 99 removed outlier: 3.608A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA F 40 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 45 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 100 through 102 removed outlier: 4.205A pdb=" N ILE F 100 " --> pdb=" O PRO F 107 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 126 through 128 removed outlier: 3.647A pdb=" N VAL F 141 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 197 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.758A pdb=" N GLY F 211 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 175 " --> pdb=" O TRP F 162 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 164 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU F 173 " --> pdb=" O LEU F 164 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1038 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: 2.70 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2852 1.35 - 1.47: 2285 1.47 - 1.60: 3826 1.60 - 1.72: 3 1.72 - 1.84: 83 Bond restraints: 9049 Sorted by residual: bond pdb=" C11 9UJ C 401 " pdb=" S02 9UJ C 401 " ideal model delta sigma weight residual 1.484 1.808 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C10 9UJ C 401 " pdb=" S02 9UJ C 401 " ideal model delta sigma weight residual 1.642 1.844 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C09 9UJ C 401 " pdb=" C14 9UJ C 401 " ideal model delta sigma weight residual 1.435 1.602 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C10 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.611 1.471 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C09 9UJ C 401 " pdb=" N07 9UJ C 401 " ideal model delta sigma weight residual 1.451 1.564 -0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 93.16 - 104.31: 105 104.31 - 115.47: 5637 115.47 - 126.62: 6381 126.62 - 137.78: 150 137.78 - 148.94: 1 Bond angle restraints: 12274 Sorted by residual: angle pdb=" C PHE C 73 " pdb=" N ARG C 74 " pdb=" CA ARG C 74 " ideal model delta sigma weight residual 121.70 148.94 -27.24 1.80e+00 3.09e-01 2.29e+02 angle pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta sigma weight residual 119.84 131.77 -11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 109.81 129.39 -19.58 2.21e+00 2.05e-01 7.85e+01 angle pdb=" C PRO F 222 " pdb=" CA PRO F 222 " pdb=" CB PRO F 222 " ideal model delta sigma weight residual 111.56 125.73 -14.17 1.65e+00 3.67e-01 7.38e+01 angle pdb=" C13 9UJ C 401 " pdb=" C15 9UJ C 401 " pdb=" C19 9UJ C 401 " ideal model delta sigma weight residual 101.20 122.24 -21.04 3.00e+00 1.11e-01 4.92e+01 ... (remaining 12269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 4794 23.85 - 47.69: 469 47.69 - 71.54: 63 71.54 - 95.39: 7 95.39 - 119.23: 1 Dihedral angle restraints: 5334 sinusoidal: 2058 harmonic: 3276 Sorted by residual: dihedral pdb=" CA TYR F 221 " pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta harmonic sigma weight residual 180.00 60.77 119.23 0 5.00e+00 4.00e-02 5.69e+02 dihedral pdb=" C TYR F 221 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual -122.60 -149.63 27.03 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual 122.80 149.59 -26.79 0 2.50e+00 1.60e-01 1.15e+02 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 1388 0.250 - 0.500: 0 0.500 - 0.750: 0 0.750 - 1.000: 2 1.000 - 1.250: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA TYR F 221 " pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CB TYR F 221 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA PHE C 73 " pdb=" N PHE C 73 " pdb=" C PHE C 73 " pdb=" CB PHE C 73 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" C PRO F 222 " pdb=" CB PRO F 222 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 1388 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 233 " -0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 234 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 221 " -0.064 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO F 222 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 275 " -0.014 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE C 275 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE C 275 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 276 " -0.015 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 86 2.60 - 3.18: 6996 3.18 - 3.75: 13768 3.75 - 4.33: 18835 4.33 - 4.90: 31806 Nonbonded interactions: 71491 Sorted by model distance: nonbonded pdb=" OE2 GLU A 258 " pdb=" OG1 THR A 261 " model vdw 2.029 2.440 nonbonded pdb=" O ILE C 16 " pdb=" OG1 THR C 20 " model vdw 2.166 2.440 nonbonded pdb=" O SER A 96 " pdb=" OG SER A 96 " model vdw 2.226 2.440 nonbonded pdb=" O GLN C 148 " pdb=" OG1 THR C 152 " model vdw 2.257 2.440 nonbonded pdb=" O GLN A 73 " pdb=" OG SER A 96 " model vdw 2.271 2.440 ... (remaining 71486 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=0.04 max=1.00 mean=0.99 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: 0.740 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: 26.720 Find NCS groups from input model: 0.220 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.006 0.324 9049 Z= 0.331 Angle : 0.744 27.235 12274 Z= 0.352 Chirality : 0.061 1.250 1391 Planarity : 0.005 0.122 1552 Dihedral : 17.868 119.232 3218 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.42 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 31.07 % Favored : 68.93 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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: 1.17 (0.26), residues: 1116 helix: 1.69 (0.26), residues: 397 sheet: 1.36 (0.32), residues: 298 loop : -0.52 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 75 HIS 0.002 0.000 HIS F 35 PHE 0.020 0.001 PHE C 197 TYR 0.007 0.001 TYR F 221 ARG 0.007 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6877 (m-30) cc_final: 0.6655 (m-30) REVERT: C 120 SER cc_start: 0.7960 (m) cc_final: 0.7505 (p) REVERT: F 183 SER cc_start: 0.8246 (m) cc_final: 0.7935 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2590 time to fit residues: 57.0198 Evaluate side-chains 153 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9049 Z= 0.266 Angle : 0.631 16.284 12274 Z= 0.322 Chirality : 0.044 0.277 1391 Planarity : 0.004 0.067 1552 Dihedral : 4.723 60.721 1232 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.23 % Favored : 96.42 % Rotamer: Outliers : 3.56 % Allowed : 28.77 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.86 % Twisted General : 0.09 % 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 (0.25), residues: 1116 helix: 1.77 (0.26), residues: 389 sheet: 1.01 (0.30), residues: 307 loop : -0.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 47 HIS 0.004 0.001 HIS B 244 PHE 0.017 0.002 PHE A 239 TYR 0.014 0.001 TYR F 50 ARG 0.005 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 0.974 Fit side-chains REVERT: A 17 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5606 (ttm110) REVERT: A 25 ASP cc_start: 0.6971 (m-30) cc_final: 0.6709 (m-30) REVERT: B 29 LYS cc_start: 0.7935 (tttm) cc_final: 0.7598 (ttmm) REVERT: C 12 MET cc_start: 0.6779 (mmp) cc_final: 0.6480 (mmp) REVERT: C 29 LEU cc_start: 0.7448 (tp) cc_final: 0.7245 (tt) REVERT: C 120 SER cc_start: 0.8067 (m) cc_final: 0.7633 (p) REVERT: F 183 SER cc_start: 0.8222 (m) cc_final: 0.7910 (p) outliers start: 34 outliers final: 19 residues processed: 198 average time/residue: 0.2105 time to fit residues: 57.2692 Evaluate side-chains 188 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 228 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 9049 Z= 0.337 Angle : 0.636 16.214 12274 Z= 0.323 Chirality : 0.045 0.286 1391 Planarity : 0.004 0.062 1552 Dihedral : 4.993 67.399 1232 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.49 % Favored : 96.06 % Rotamer: Outliers : 4.81 % Allowed : 28.24 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1116 helix: 1.60 (0.26), residues: 389 sheet: 0.76 (0.30), residues: 300 loop : -0.79 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 47 HIS 0.005 0.001 HIS B 244 PHE 0.019 0.002 PHE A 239 TYR 0.014 0.002 TYR A 83 ARG 0.007 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 0.972 Fit side-chains REVERT: A 17 ARG cc_start: 0.5912 (mtm110) cc_final: 0.5681 (ttm110) REVERT: A 25 ASP cc_start: 0.7129 (m-30) cc_final: 0.6857 (m-30) REVERT: A 47 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.8044 (mpt180) REVERT: A 153 ASN cc_start: 0.8218 (t0) cc_final: 0.7969 (t0) REVERT: B 8 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7587 (mt-10) REVERT: B 200 ASP cc_start: 0.8032 (t0) cc_final: 0.7832 (t0) REVERT: C 29 LEU cc_start: 0.7500 (tp) cc_final: 0.7245 (tt) REVERT: C 120 SER cc_start: 0.8161 (m) cc_final: 0.7691 (p) REVERT: C 136 MET cc_start: 0.6528 (mmt) cc_final: 0.6315 (mmm) REVERT: F 125 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (p) REVERT: F 183 SER cc_start: 0.8172 (m) cc_final: 0.7843 (p) REVERT: F 205 LEU cc_start: 0.8255 (mt) cc_final: 0.7929 (mm) outliers start: 46 outliers final: 31 residues processed: 193 average time/residue: 0.2273 time to fit residues: 58.7534 Evaluate side-chains 193 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9049 Z= 0.198 Angle : 0.557 15.778 12274 Z= 0.286 Chirality : 0.042 0.295 1391 Planarity : 0.004 0.090 1552 Dihedral : 4.730 63.537 1232 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.41 % Favored : 96.15 % Rotamer: Outliers : 4.71 % Allowed : 28.97 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.75 (0.25), residues: 1116 helix: 1.73 (0.27), residues: 390 sheet: 0.66 (0.30), residues: 300 loop : -0.76 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.003 0.001 HIS F 35 PHE 0.013 0.001 PHE A 149 TYR 0.012 0.001 TYR F 221 ARG 0.004 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5912 (mtm110) cc_final: 0.5671 (ttm110) REVERT: A 47 ARG cc_start: 0.8328 (mmt-90) cc_final: 0.8014 (mpt180) REVERT: A 153 ASN cc_start: 0.8191 (t0) cc_final: 0.7896 (t0) REVERT: B 8 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 29 LEU cc_start: 0.7442 (tp) cc_final: 0.7223 (tt) REVERT: C 120 SER cc_start: 0.8169 (m) cc_final: 0.7767 (p) REVERT: F 125 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8540 (p) REVERT: F 183 SER cc_start: 0.8187 (m) cc_final: 0.7843 (p) REVERT: F 205 LEU cc_start: 0.8227 (mt) cc_final: 0.7901 (mm) outliers start: 45 outliers final: 31 residues processed: 195 average time/residue: 0.2241 time to fit residues: 59.2259 Evaluate side-chains 198 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.0000 chunk 21 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9049 Z= 0.246 Angle : 0.578 16.092 12274 Z= 0.295 Chirality : 0.043 0.281 1391 Planarity : 0.004 0.086 1552 Dihedral : 4.704 64.143 1232 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.23 % Favored : 96.42 % Rotamer: Outliers : 4.81 % Allowed : 29.39 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.65 (0.25), residues: 1116 helix: 1.72 (0.27), residues: 387 sheet: 0.53 (0.30), residues: 294 loop : -0.79 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 134 HIS 0.004 0.001 HIS B 244 PHE 0.014 0.002 PHE A 149 TYR 0.010 0.001 TYR F 101 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5936 (mtm110) cc_final: 0.5682 (ttm110) REVERT: A 47 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8052 (mpt180) REVERT: A 153 ASN cc_start: 0.8258 (t0) cc_final: 0.8027 (t0) REVERT: A 157 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 8 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 29 LEU cc_start: 0.7452 (tp) cc_final: 0.7249 (tt) REVERT: C 120 SER cc_start: 0.8168 (m) cc_final: 0.7732 (p) REVERT: F 125 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8530 (p) REVERT: F 139 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: F 183 SER cc_start: 0.8181 (m) cc_final: 0.7832 (p) outliers start: 46 outliers final: 37 residues processed: 199 average time/residue: 0.2251 time to fit residues: 60.7755 Evaluate side-chains 206 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 139 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9049 Z= 0.264 Angle : 0.589 15.976 12274 Z= 0.299 Chirality : 0.043 0.275 1391 Planarity : 0.004 0.086 1552 Dihedral : 4.746 65.526 1232 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.58 % Favored : 96.06 % Rotamer: Outliers : 5.54 % Allowed : 29.08 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.55 (0.25), residues: 1116 helix: 1.61 (0.26), residues: 396 sheet: 0.42 (0.29), residues: 294 loop : -0.82 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 98 HIS 0.004 0.001 HIS B 244 PHE 0.015 0.002 PHE A 149 TYR 0.010 0.001 TYR F 101 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5961 (mtm110) cc_final: 0.5708 (ttm110) REVERT: A 44 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6234 (mtp180) REVERT: A 47 ARG cc_start: 0.8365 (mmt-90) cc_final: 0.8069 (mpt180) REVERT: A 144 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 153 ASN cc_start: 0.8340 (t0) cc_final: 0.8094 (t0) REVERT: A 157 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (m) REVERT: C 29 LEU cc_start: 0.7462 (tp) cc_final: 0.7261 (tt) REVERT: C 120 SER cc_start: 0.8188 (m) cc_final: 0.7794 (p) REVERT: F 125 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (p) REVERT: F 183 SER cc_start: 0.8177 (m) cc_final: 0.7830 (p) outliers start: 53 outliers final: 41 residues processed: 198 average time/residue: 0.2272 time to fit residues: 60.5264 Evaluate side-chains 208 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9049 Z= 0.268 Angle : 0.594 15.820 12274 Z= 0.301 Chirality : 0.043 0.269 1391 Planarity : 0.004 0.083 1552 Dihedral : 4.812 67.840 1232 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 5.96 % Allowed : 28.66 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.51 (0.25), residues: 1116 helix: 1.66 (0.26), residues: 394 sheet: 0.33 (0.29), residues: 294 loop : -0.86 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.004 0.001 HIS A 89 PHE 0.014 0.002 PHE A 149 TYR 0.011 0.001 TYR F 101 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5941 (mtm110) cc_final: 0.5695 (ttm110) REVERT: A 44 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6231 (mtp180) REVERT: A 47 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.8123 (mpt180) REVERT: A 157 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8283 (m) REVERT: A 302 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7262 (ttm170) REVERT: C 120 SER cc_start: 0.8204 (m) cc_final: 0.7748 (p) REVERT: C 175 VAL cc_start: 0.6551 (p) cc_final: 0.6345 (t) REVERT: F 106 SER cc_start: 0.1533 (OUTLIER) cc_final: 0.0572 (t) REVERT: F 183 SER cc_start: 0.8172 (m) cc_final: 0.7835 (p) outliers start: 57 outliers final: 43 residues processed: 207 average time/residue: 0.2368 time to fit residues: 66.0917 Evaluate side-chains 214 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 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 237 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9049 Z= 0.228 Angle : 0.585 15.609 12274 Z= 0.295 Chirality : 0.042 0.253 1391 Planarity : 0.004 0.082 1552 Dihedral : 4.746 67.446 1232 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.23 % Favored : 96.42 % Rotamer: Outliers : 5.54 % Allowed : 29.29 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.54 (0.25), residues: 1116 helix: 1.69 (0.26), residues: 393 sheet: 0.31 (0.29), residues: 294 loop : -0.82 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 134 HIS 0.003 0.001 HIS A 89 PHE 0.014 0.002 PHE A 149 TYR 0.010 0.001 TYR F 101 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5949 (mtm110) cc_final: 0.5706 (ttm110) REVERT: A 44 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6222 (mtp180) REVERT: A 47 ARG cc_start: 0.8414 (mmt-90) cc_final: 0.8121 (mpt180) REVERT: A 302 ARG cc_start: 0.7531 (ttm170) cc_final: 0.7266 (ttm170) REVERT: C 120 SER cc_start: 0.8192 (m) cc_final: 0.7805 (p) REVERT: F 183 SER cc_start: 0.8178 (m) cc_final: 0.7842 (p) outliers start: 53 outliers final: 48 residues processed: 202 average time/residue: 0.2321 time to fit residues: 62.8334 Evaluate side-chains 218 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.0170 chunk 64 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9049 Z= 0.192 Angle : 0.562 12.618 12274 Z= 0.281 Chirality : 0.042 0.172 1391 Planarity : 0.004 0.069 1552 Dihedral : 4.711 66.051 1232 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 5.02 % Allowed : 29.50 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.62 (0.25), residues: 1116 helix: 1.78 (0.26), residues: 392 sheet: 0.34 (0.29), residues: 295 loop : -0.79 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 75 HIS 0.003 0.001 HIS A 140 PHE 0.012 0.001 PHE A 149 TYR 0.017 0.001 TYR F 221 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5961 (mtm110) cc_final: 0.5716 (ttm110) REVERT: A 44 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6218 (mtp180) REVERT: A 47 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8111 (mpt180) REVERT: A 302 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7230 (ttm170) REVERT: C 120 SER cc_start: 0.8216 (m) cc_final: 0.7783 (p) REVERT: C 206 MET cc_start: 0.8245 (tpp) cc_final: 0.7953 (mmm) REVERT: C 229 LEU cc_start: 0.7181 (tp) cc_final: 0.6867 (tp) REVERT: F 183 SER cc_start: 0.8180 (m) cc_final: 0.7840 (p) outliers start: 48 outliers final: 45 residues processed: 197 average time/residue: 0.2314 time to fit residues: 60.8924 Evaluate side-chains 216 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9049 Z= 0.196 Angle : 0.548 10.936 12274 Z= 0.275 Chirality : 0.042 0.172 1391 Planarity : 0.004 0.079 1552 Dihedral : 4.699 65.663 1232 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 5.23 % Allowed : 29.71 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.61 (0.25), residues: 1116 helix: 1.78 (0.26), residues: 393 sheet: 0.28 (0.29), residues: 295 loop : -0.75 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 134 HIS 0.003 0.001 HIS A 140 PHE 0.012 0.001 PHE A 149 TYR 0.010 0.001 TYR F 221 ARG 0.002 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5973 (mtm110) cc_final: 0.5721 (ttm110) REVERT: A 44 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6213 (mtp180) REVERT: A 47 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8098 (mpt180) REVERT: A 302 ARG cc_start: 0.7523 (ttm170) cc_final: 0.7236 (ttm170) REVERT: C 120 SER cc_start: 0.8213 (m) cc_final: 0.7836 (p) REVERT: C 206 MET cc_start: 0.8263 (tpp) cc_final: 0.7997 (mmm) REVERT: C 229 LEU cc_start: 0.7114 (tp) cc_final: 0.6761 (tp) REVERT: F 183 SER cc_start: 0.8180 (m) cc_final: 0.7840 (p) outliers start: 50 outliers final: 45 residues processed: 199 average time/residue: 0.2230 time to fit residues: 59.8910 Evaluate side-chains 217 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115244 restraints weight = 12757.942| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.77 r_work: 0.3346 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9049 Z= 0.192 Angle : 0.545 10.668 12274 Z= 0.273 Chirality : 0.041 0.178 1391 Planarity : 0.004 0.076 1552 Dihedral : 4.703 66.595 1232 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 4.92 % Allowed : 30.02 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.63 (0.25), residues: 1116 helix: 1.80 (0.27), residues: 392 sheet: 0.28 (0.29), residues: 295 loop : -0.74 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 134 HIS 0.003 0.001 HIS A 140 PHE 0.012 0.001 PHE A 149 TYR 0.010 0.001 TYR F 101 ARG 0.002 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.23 seconds wall clock time: 43 minutes 30.42 seconds (2610.42 seconds total)