Starting phenix.real_space_refine on Fri Dec 8 20:14:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6u_25728/12_2023/7t6u_25728_updated.pdb" } resolution = 2.9 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5791 2.51 5 N 1516 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "R ARG 26": "NH1" <-> "NH2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 189": "OE1" <-> "OE2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1763 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2382 Unusual residues: {'PLM': 2} Classifications: {'peptide': 299, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 285, None: 2} Not linked: pdbres="LEU R 317 " pdbres="PLM R 401 " Not linked: pdbres="PLM R 401 " pdbres="PLM R 402 " Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.11, per 1000 atoms: 0.57 Number of scatterers: 9033 At special positions: 0 Unit cell: (118.8, 115.56, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1662 8.00 N 1516 7.00 C 5791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 21 " Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 13 sheets defined 34.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.948A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.514A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.947A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.721A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.556A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.971A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.758A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.616A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 22 through 38 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 40 through 53 removed outlier: 3.757A pdb=" N VAL R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 4.121A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Proline residue: R 79 - end of helix removed outlier: 3.613A pdb=" N VAL R 83 " --> pdb=" O PRO R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 removed outlier: 3.652A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 145 removed outlier: 3.815A pdb=" N LYS R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 156 Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 190 through 206 removed outlier: 3.518A pdb=" N LEU R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 removed outlier: 3.737A pdb=" N ILE R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 252 removed outlier: 3.568A pdb=" N VAL R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 266 removed outlier: 3.730A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 274 Processing helix chain 'R' and resid 278 through 302 removed outlier: 4.521A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.594A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU R 297 " --> pdb=" O PHE R 293 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.384A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.703A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.491A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.832A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.516A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.674A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.993A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.623A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'R' and resid 164 through 168 removed outlier: 3.709A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1044 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: 2.92 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1449 1.31 - 1.43: 2518 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.81: 94 Bond restraints: 9225 Sorted by residual: bond pdb=" C QXV L 21 " pdb=" NXT QXV L 21 " ideal model delta sigma weight residual 1.339 1.445 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.48e+01 bond pdb=" N TYR R 274 " pdb=" CA TYR R 274 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.06e-02 8.90e+03 1.19e+01 bond pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N VAL R 284 " pdb=" CA VAL R 284 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.51: 145 105.51 - 112.71: 4784 112.71 - 119.92: 3302 119.92 - 127.13: 4145 127.13 - 134.34: 110 Bond angle restraints: 12486 Sorted by residual: angle pdb=" N PHE R 163 " pdb=" CA PHE R 163 " pdb=" C PHE R 163 " ideal model delta sigma weight residual 112.94 119.73 -6.79 1.41e+00 5.03e-01 2.32e+01 angle pdb=" N LEU R 263 " pdb=" CA LEU R 263 " pdb=" C LEU R 263 " ideal model delta sigma weight residual 111.82 106.40 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" C ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta sigma weight residual 113.04 120.59 -7.55 1.63e+00 3.76e-01 2.15e+01 angle pdb=" N PRO R 286 " pdb=" CA PRO R 286 " pdb=" CB PRO R 286 " ideal model delta sigma weight residual 103.33 98.30 5.03 1.10e+00 8.26e-01 2.09e+01 angle pdb=" CA CYS R 176 " pdb=" C CYS R 176 " pdb=" O CYS R 176 " ideal model delta sigma weight residual 121.58 116.47 5.11 1.12e+00 7.97e-01 2.08e+01 ... (remaining 12481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4947 16.90 - 33.80: 411 33.80 - 50.70: 76 50.70 - 67.60: 11 67.60 - 84.50: 5 Dihedral angle restraints: 5450 sinusoidal: 2131 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -170.50 84.50 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CA GLU A 276 " pdb=" C GLU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" C ASN R 285 " pdb=" N ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta harmonic sigma weight residual -122.60 -137.44 14.84 0 2.50e+00 1.60e-01 3.52e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1278 0.098 - 0.196: 127 0.196 - 0.293: 11 0.293 - 0.391: 4 0.391 - 0.489: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ASN R 285 " pdb=" N ASN R 285 " pdb=" C ASN R 285 " pdb=" CB ASN R 285 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA GLU R 270 " pdb=" N GLU R 270 " pdb=" C GLU R 270 " pdb=" CB GLU R 270 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1419 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO R 149 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 238 " 0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 239 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO R 256 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.038 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2879 2.83 - 3.35: 7763 3.35 - 3.87: 15088 3.87 - 4.38: 17860 4.38 - 4.90: 30664 Nonbonded interactions: 74254 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" OG SER A 281 " model vdw 2.315 2.440 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.334 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.335 2.440 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.346 2.440 nonbonded pdb=" OE2 GLU A 28 " pdb=" OG SER R 140 " model vdw 2.347 2.440 ... (remaining 74249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.140 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.320 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 0.106 9225 Z= 0.368 Angle : 1.000 9.546 12486 Z= 0.635 Chirality : 0.064 0.489 1422 Planarity : 0.007 0.069 1565 Dihedral : 12.927 81.902 3301 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.84 (0.20), residues: 1133 helix: -4.08 (0.14), residues: 399 sheet: -0.94 (0.28), residues: 284 loop : -1.88 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 132 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE R 163 TYR 0.025 0.002 TYR R 175 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 248 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 1.1230 time to fit residues: 301.2363 Evaluate side-chains 199 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 101 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 62 HIS B 155 ASN B 230 ASN B 237 ASN B 239 ASN B 293 ASN E 82 GLN R 108 ASN R 136 HIS R 258 GLN R 307 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9225 Z= 0.156 Angle : 0.548 10.187 12486 Z= 0.285 Chirality : 0.042 0.127 1422 Planarity : 0.005 0.052 1565 Dihedral : 5.132 73.169 1265 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.36 % Allowed : 14.68 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.86 (0.22), residues: 1133 helix: -1.48 (0.22), residues: 405 sheet: -0.53 (0.29), residues: 286 loop : -1.25 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS R 136 PHE 0.010 0.001 PHE B 235 TYR 0.011 0.001 TYR B 264 ARG 0.008 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 1.062 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 236 average time/residue: 1.1637 time to fit residues: 293.2394 Evaluate side-chains 215 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.5688 time to fit residues: 5.9453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 237 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN R 66 ASN R 102 HIS R 315 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9225 Z= 0.168 Angle : 0.527 8.212 12486 Z= 0.269 Chirality : 0.041 0.141 1422 Planarity : 0.004 0.047 1565 Dihedral : 4.745 66.060 1265 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.28 % Allowed : 16.82 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1133 helix: -0.01 (0.25), residues: 407 sheet: -0.43 (0.29), residues: 272 loop : -0.93 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 136 PHE 0.011 0.001 PHE B 235 TYR 0.009 0.001 TYR E 190 ARG 0.008 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 0.964 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 236 average time/residue: 1.1424 time to fit residues: 288.3571 Evaluate side-chains 213 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.1498 time to fit residues: 2.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.0040 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9225 Z= 0.159 Angle : 0.513 8.773 12486 Z= 0.261 Chirality : 0.041 0.147 1422 Planarity : 0.004 0.044 1565 Dihedral : 4.555 62.786 1265 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.79 % Allowed : 17.74 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1133 helix: 0.62 (0.27), residues: 410 sheet: -0.18 (0.30), residues: 271 loop : -0.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.029 0.001 PHE E 68 TYR 0.013 0.001 TYR A 230 ARG 0.005 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 1.100 Fit side-chains outliers start: 47 outliers final: 24 residues processed: 225 average time/residue: 1.1281 time to fit residues: 272.0071 Evaluate side-chains 222 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.3017 time to fit residues: 4.2891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9225 Z= 0.199 Angle : 0.540 10.009 12486 Z= 0.270 Chirality : 0.042 0.178 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.520 61.042 1265 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.08 % Allowed : 19.57 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1133 helix: 0.90 (0.27), residues: 410 sheet: -0.09 (0.30), residues: 281 loop : -0.73 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.025 0.001 PHE E 68 TYR 0.012 0.001 TYR B 111 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 228 average time/residue: 1.2110 time to fit residues: 294.9830 Evaluate side-chains 219 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.5099 time to fit residues: 5.9754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.0020 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 0.0010 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 331 ASN B 155 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9225 Z= 0.158 Angle : 0.527 10.390 12486 Z= 0.262 Chirality : 0.041 0.178 1422 Planarity : 0.003 0.042 1565 Dihedral : 4.431 60.027 1265 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.67 % Allowed : 21.30 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1133 helix: 1.15 (0.27), residues: 411 sheet: 0.09 (0.31), residues: 269 loop : -0.66 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.026 0.001 PHE E 68 TYR 0.013 0.001 TYR B 111 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 223 average time/residue: 1.2012 time to fit residues: 285.7721 Evaluate side-chains 223 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.2325 time to fit residues: 3.8451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9225 Z= 0.251 Angle : 0.565 9.639 12486 Z= 0.282 Chirality : 0.043 0.184 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.567 60.171 1265 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.26 % Allowed : 21.92 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1133 helix: 1.05 (0.27), residues: 410 sheet: 0.05 (0.31), residues: 271 loop : -0.62 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 62 PHE 0.028 0.001 PHE E 68 TYR 0.013 0.001 TYR B 111 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 223 average time/residue: 1.1419 time to fit residues: 272.2261 Evaluate side-chains 222 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.5349 time to fit residues: 6.1718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9225 Z= 0.173 Angle : 0.552 11.424 12486 Z= 0.272 Chirality : 0.042 0.181 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.484 59.653 1265 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.06 % Allowed : 22.02 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1133 helix: 1.21 (0.28), residues: 405 sheet: 0.10 (0.31), residues: 270 loop : -0.66 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.033 0.001 PHE E 68 TYR 0.014 0.001 TYR B 111 ARG 0.014 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 231 average time/residue: 1.1358 time to fit residues: 280.8379 Evaluate side-chains 224 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 0.4343 time to fit residues: 3.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.0570 chunk 30 optimal weight: 0.0020 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 155 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9225 Z= 0.132 Angle : 0.533 12.928 12486 Z= 0.264 Chirality : 0.041 0.189 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.340 58.736 1265 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.24 % Allowed : 22.73 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1133 helix: 1.38 (0.28), residues: 407 sheet: 0.10 (0.31), residues: 267 loop : -0.63 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.031 0.001 PHE E 68 TYR 0.013 0.001 TYR B 111 ARG 0.015 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.015 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 20 residues processed: 222 average time/residue: 1.2299 time to fit residues: 291.8748 Evaluate side-chains 219 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.1792 time to fit residues: 2.1795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9225 Z= 0.176 Angle : 0.565 12.433 12486 Z= 0.279 Chirality : 0.042 0.179 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.397 58.209 1265 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.04 % Allowed : 24.16 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1133 helix: 1.34 (0.28), residues: 406 sheet: 0.23 (0.31), residues: 274 loop : -0.66 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.029 0.001 PHE E 68 TYR 0.010 0.001 TYR B 111 ARG 0.016 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 0.907 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 213 average time/residue: 1.2171 time to fit residues: 276.3435 Evaluate side-chains 214 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.1921 time to fit residues: 1.8800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102683 restraints weight = 12319.481| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.75 r_work: 0.3188 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9225 Z= 0.261 Angle : 0.594 12.040 12486 Z= 0.295 Chirality : 0.044 0.186 1422 Planarity : 0.004 0.041 1565 Dihedral : 4.603 57.828 1265 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.14 % Allowed : 24.16 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1133 helix: 1.20 (0.27), residues: 406 sheet: 0.16 (0.31), residues: 271 loop : -0.65 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.045 0.002 PHE E 68 TYR 0.015 0.001 TYR B 111 ARG 0.016 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4532.65 seconds wall clock time: 80 minutes 47.13 seconds (4847.13 seconds total)