Starting phenix.real_space_refine on Sat Apr 6 23:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/04_2024/8jiu_36328_updated.pdb" } resolution = 2.76 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= -0.000 sd= 0.019 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 57 5.16 5 C 5767 2.51 5 N 1588 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9075 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1875 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2548 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3018 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 9075 At special positions: 0 Unit cell: (78.183, 100.674, 171.36, 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 57 16.00 O 1663 8.00 N 1588 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.01 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN P 2 " Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 35.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.863A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'P' and resid 4 through 27 Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.130A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.662A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 30 through 47 removed outlier: 3.614A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 90 removed outlier: 4.312A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS R 90 " --> pdb=" O TRP R 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 86 through 90' Processing helix chain 'R' and resid 118 through 120 No H-bonds generated for 'chain 'R' and resid 118 through 120' Processing helix chain 'R' and resid 125 through 165 removed outlier: 3.768A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.784A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 215 Processing helix chain 'R' and resid 221 through 251 removed outlier: 3.700A pdb=" N GLY R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 270 Processing helix chain 'R' and resid 272 through 288 removed outlier: 4.371A pdb=" N MET R 276 " --> pdb=" O TRP R 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 305 through 307 No H-bonds generated for 'chain 'R' and resid 305 through 307' Processing helix chain 'R' and resid 309 through 335 removed outlier: 4.077A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 352 Processing helix chain 'R' and resid 355 through 357 No H-bonds generated for 'chain 'R' and resid 355 through 357' Processing helix chain 'R' and resid 361 through 364 Processing helix chain 'R' and resid 375 through 401 removed outlier: 3.763A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.409A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.842A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.647A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.329A 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: 7.267A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A 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: 6.850A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.287A 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: 6.435A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.593A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.245A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 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: 2.67 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 2512 1.45 - 1.57: 4931 1.57 - 1.70: 2 1.70 - 1.82: 78 Bond restraints: 9272 Sorted by residual: bond pdb=" CA PHE R 365 " pdb=" C PHE R 365 " ideal model delta sigma weight residual 1.533 1.493 0.040 5.60e-03 3.19e+04 5.19e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.371 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " ideal model delta sigma weight residual 1.538 1.623 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" N ARG R 94 " pdb=" CA ARG R 94 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.23e-02 6.61e+03 1.64e+01 bond pdb=" C HIS P 1 " pdb=" N DSN P 2 " ideal model delta sigma weight residual 1.329 1.382 -0.053 1.40e-02 5.10e+03 1.45e+01 ... (remaining 9267 not shown) Histogram of bond angle deviations from ideal: 93.65 - 102.48: 36 102.48 - 111.31: 3885 111.31 - 120.15: 4631 120.15 - 128.98: 3942 128.98 - 137.81: 89 Bond angle restraints: 12583 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 93.65 24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" N LEU B 30 " pdb=" CA LEU B 30 " pdb=" C LEU B 30 " ideal model delta sigma weight residual 113.43 104.11 9.32 1.26e+00 6.30e-01 5.47e+01 angle pdb=" N LEU R 47 " pdb=" CA LEU R 47 " pdb=" C LEU R 47 " ideal model delta sigma weight residual 112.23 102.92 9.31 1.26e+00 6.30e-01 5.46e+01 angle pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta sigma weight residual 110.50 115.02 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY R 196 " pdb=" CA GLY R 196 " pdb=" C GLY R 196 " ideal model delta sigma weight residual 112.50 104.46 8.04 1.16e+00 7.43e-01 4.81e+01 ... (remaining 12578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4709 17.30 - 34.60: 472 34.60 - 51.90: 208 51.90 - 69.20: 67 69.20 - 86.50: 16 Dihedral angle restraints: 5472 sinusoidal: 2062 harmonic: 3410 Sorted by residual: dihedral pdb=" C VAL R 280 " pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual -122.00 -138.87 16.87 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual 123.40 138.75 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -39.94 -46.06 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 5469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1300 0.119 - 0.238: 93 0.238 - 0.357: 12 0.357 - 0.476: 3 0.476 - 0.595: 4 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA VAL R 280 " pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CB VAL R 280 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 1409 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 52 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR C 52 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 52 " -0.036 2.00e-02 2.50e+03 pdb=" N PRO C 53 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C04 D6M P 101 " -0.038 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " -0.031 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " 0.047 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA DSN P 2 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C DSN P 2 " -0.058 2.00e-02 2.50e+03 pdb=" O DSN P 2 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN P 3 " 0.019 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1590 2.75 - 3.29: 8806 3.29 - 3.83: 15474 3.83 - 4.36: 17996 4.36 - 4.90: 30063 Nonbonded interactions: 73929 Sorted by model distance: nonbonded pdb=" N GLN R 120 " pdb=" OE1 GLN R 120 " model vdw 2.217 2.520 nonbonded pdb=" O SER R 203 " pdb=" OG SER R 203 " model vdw 2.254 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.265 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.311 2.440 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.318 2.440 ... (remaining 73924 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.040 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.124 9272 Z= 0.486 Angle : 1.140 24.390 12583 Z= 0.729 Chirality : 0.075 0.595 1412 Planarity : 0.006 0.080 1610 Dihedral : 18.352 86.500 3250 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 1.29 % Allowed : 6.38 % Favored : 92.33 % Rotamer: Outliers : 15.73 % Allowed : 7.54 % Favored : 76.72 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.23), residues: 1160 helix: -1.51 (0.24), residues: 437 sheet: -1.35 (0.35), residues: 211 loop : -1.99 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 241 HIS 0.007 0.001 HIS B 91 PHE 0.024 0.002 PHE N 68 TYR 0.019 0.001 TYR R 145 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 193 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 294 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: P 21 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8074 (t0) REVERT: P 25 TRP cc_start: 0.8655 (t60) cc_final: 0.7569 (t60) REVERT: B 10 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (mm-30) REVERT: B 17 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8708 (tm-30) REVERT: B 251 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8557 (mtt90) REVERT: B 259 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: B 301 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8034 (mmmm) REVERT: C 17 GLU cc_start: 0.9309 (tp30) cc_final: 0.8584 (tm-30) REVERT: C 21 MET cc_start: 0.9221 (mmp) cc_final: 0.9009 (mmm) REVERT: C 26 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (p0) REVERT: C 28 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 32 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8242 (tppt) REVERT: N 18 LEU cc_start: 0.8435 (mt) cc_final: 0.8176 (mt) REVERT: N 28 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (p) REVERT: N 73 ASP cc_start: 0.8249 (t70) cc_final: 0.7858 (t0) REVERT: R 28 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8095 (m) REVERT: R 30 ASP cc_start: 0.9594 (OUTLIER) cc_final: 0.9256 (p0) REVERT: R 39 TYR cc_start: 0.8495 (t80) cc_final: 0.8155 (t80) REVERT: R 88 HIS cc_start: 0.7919 (t-90) cc_final: 0.7692 (t-90) REVERT: R 123 MET cc_start: 0.7428 (mmt) cc_final: 0.7005 (mmm) REVERT: R 144 MET cc_start: 0.9261 (tmm) cc_final: 0.8503 (tmm) REVERT: R 145 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8013 (p90) REVERT: R 201 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7789 (ttt90) REVERT: R 211 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8993 (p) REVERT: R 231 MET cc_start: 0.9036 (ttp) cc_final: 0.8581 (ttp) REVERT: R 251 ASN cc_start: 0.8744 (t0) cc_final: 0.8120 (t0) REVERT: R 287 CYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8813 (t) REVERT: R 293 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: R 368 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8560 (t) REVERT: R 385 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (t0) REVERT: R 405 LYS cc_start: 0.9022 (mmpt) cc_final: 0.8616 (mmmt) outliers start: 146 outliers final: 21 residues processed: 287 average time/residue: 1.2332 time to fit residues: 377.0460 Evaluate side-chains 189 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 58 CYS Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 201 ARG Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 265 SER Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 GLN Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN C 18 GLN R 46 ASN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9272 Z= 0.211 Angle : 0.657 9.967 12583 Z= 0.342 Chirality : 0.043 0.313 1412 Planarity : 0.005 0.070 1610 Dihedral : 10.048 99.376 1373 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.69 % Favored : 93.97 % Rotamer: Outliers : 4.63 % Allowed : 19.29 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.24), residues: 1160 helix: 0.13 (0.26), residues: 429 sheet: -0.86 (0.34), residues: 209 loop : -1.75 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 418 HIS 0.006 0.001 HIS R 45 PHE 0.011 0.001 PHE R 97 TYR 0.023 0.001 TYR R 145 ARG 0.007 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8332 (mm-30) REVERT: A 228 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7748 (mtp85) REVERT: A 294 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: P 21 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7350 (t0) REVERT: P 26 LEU cc_start: 0.9468 (tp) cc_final: 0.8732 (tp) REVERT: B 12 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8787 (pp20) REVERT: B 17 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8758 (tm-30) REVERT: B 84 SER cc_start: 0.8911 (t) cc_final: 0.8685 (p) REVERT: B 301 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8186 (mmmm) REVERT: C 17 GLU cc_start: 0.9291 (tp30) cc_final: 0.8454 (tp30) REVERT: C 21 MET cc_start: 0.9096 (mmp) cc_final: 0.8562 (mmm) REVERT: C 28 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8405 (pp) REVERT: C 32 LYS cc_start: 0.8948 (tptp) cc_final: 0.8282 (tppt) REVERT: C 42 GLU cc_start: 0.8695 (pp20) cc_final: 0.8399 (pm20) REVERT: C 44 HIS cc_start: 0.6377 (OUTLIER) cc_final: 0.6111 (p-80) REVERT: N 18 LEU cc_start: 0.8485 (mt) cc_final: 0.8275 (mt) REVERT: N 73 ASP cc_start: 0.8193 (t70) cc_final: 0.7642 (t0) REVERT: R 31 PHE cc_start: 0.9248 (m-80) cc_final: 0.9003 (m-80) REVERT: R 39 TYR cc_start: 0.8457 (t80) cc_final: 0.8112 (t80) REVERT: R 108 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8845 (mmp80) REVERT: R 170 HIS cc_start: 0.5721 (OUTLIER) cc_final: 0.4632 (t70) REVERT: R 231 MET cc_start: 0.8950 (ttp) cc_final: 0.8601 (ttp) REVERT: R 405 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8631 (mmmt) outliers start: 43 outliers final: 17 residues processed: 178 average time/residue: 1.2911 time to fit residues: 244.9013 Evaluate side-chains 165 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 294 GLN P 13 GLN N 120 GLN R 45 HIS ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9272 Z= 0.206 Angle : 0.607 8.864 12583 Z= 0.313 Chirality : 0.042 0.315 1412 Planarity : 0.004 0.061 1610 Dihedral : 7.576 87.839 1326 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.40 % Favored : 95.26 % Rotamer: Outliers : 3.99 % Allowed : 21.98 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.25), residues: 1160 helix: 0.66 (0.26), residues: 442 sheet: -0.53 (0.34), residues: 224 loop : -1.65 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 115 HIS 0.009 0.001 HIS R 45 PHE 0.011 0.001 PHE P 22 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7877 (mtp85) REVERT: A 294 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: P 21 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7243 (t0) REVERT: P 26 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9090 (tp) REVERT: B 10 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9149 (tp30) REVERT: B 12 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8870 (pp20) REVERT: C 17 GLU cc_start: 0.9290 (tp30) cc_final: 0.7994 (tp30) REVERT: C 21 MET cc_start: 0.9123 (mmp) cc_final: 0.8755 (mmm) REVERT: C 28 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8299 (pp) REVERT: C 32 LYS cc_start: 0.8975 (tptp) cc_final: 0.8411 (tppt) REVERT: C 44 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.6263 (p-80) REVERT: N 18 LEU cc_start: 0.8493 (mt) cc_final: 0.8248 (mt) REVERT: N 73 ASP cc_start: 0.8260 (t70) cc_final: 0.7594 (t0) REVERT: N 82 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7309 (tm-30) REVERT: N 83 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7809 (mtt) REVERT: R 39 TYR cc_start: 0.8457 (t80) cc_final: 0.8234 (t80) REVERT: R 115 TRP cc_start: 0.7107 (p-90) cc_final: 0.6876 (p-90) REVERT: R 124 ASP cc_start: 0.8644 (t0) cc_final: 0.8244 (p0) REVERT: R 136 LYS cc_start: 0.9254 (mmmm) cc_final: 0.9005 (mtpp) REVERT: R 170 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.4812 (t70) REVERT: R 231 MET cc_start: 0.8913 (ttp) cc_final: 0.8560 (ttp) REVERT: R 293 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: R 405 LYS cc_start: 0.9165 (mmpt) cc_final: 0.8716 (mmmt) outliers start: 37 outliers final: 16 residues processed: 168 average time/residue: 1.2799 time to fit residues: 229.4859 Evaluate side-chains 162 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 293 GLN Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 13 GLN R 44 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9272 Z= 0.205 Angle : 0.601 9.594 12583 Z= 0.307 Chirality : 0.041 0.279 1412 Planarity : 0.004 0.058 1610 Dihedral : 6.438 74.712 1314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 3.45 % Allowed : 24.35 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.25), residues: 1160 helix: 0.89 (0.26), residues: 443 sheet: -0.35 (0.35), residues: 224 loop : -1.45 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 36 HIS 0.014 0.001 HIS R 44 PHE 0.017 0.001 PHE R 33 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7905 (mtp85) REVERT: P 21 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6958 (t0) REVERT: P 26 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9140 (tp) REVERT: B 9 GLN cc_start: 0.9504 (mp10) cc_final: 0.9208 (mp10) REVERT: B 10 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9194 (tp30) REVERT: B 12 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8889 (pp20) REVERT: B 45 MET cc_start: 0.9071 (mtm) cc_final: 0.8749 (mtt) REVERT: C 17 GLU cc_start: 0.9187 (tp30) cc_final: 0.8768 (tp30) REVERT: C 20 LYS cc_start: 0.8928 (ptpt) cc_final: 0.8655 (ptpp) REVERT: C 28 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8274 (pp) REVERT: C 32 LYS cc_start: 0.8956 (tptp) cc_final: 0.8384 (tppt) REVERT: C 42 GLU cc_start: 0.8715 (pp20) cc_final: 0.8305 (pm20) REVERT: N 18 LEU cc_start: 0.8500 (mt) cc_final: 0.8269 (mt) REVERT: N 73 ASP cc_start: 0.8262 (t70) cc_final: 0.7591 (t0) REVERT: N 82 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7081 (tm-30) REVERT: R 39 TYR cc_start: 0.8859 (t80) cc_final: 0.8404 (t80) REVERT: R 115 TRP cc_start: 0.7256 (p-90) cc_final: 0.6888 (p-90) REVERT: R 136 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8993 (mtpp) REVERT: R 170 HIS cc_start: 0.5952 (OUTLIER) cc_final: 0.4886 (t70) REVERT: R 405 LYS cc_start: 0.9185 (mmpt) cc_final: 0.8740 (mmmt) outliers start: 32 outliers final: 13 residues processed: 162 average time/residue: 1.2648 time to fit residues: 218.4393 Evaluate side-chains 156 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 368 VAL Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS P 13 GLN B 88 ASN C 18 GLN N 120 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 9272 Z= 0.455 Angle : 0.717 8.868 12583 Z= 0.367 Chirality : 0.045 0.257 1412 Planarity : 0.005 0.057 1610 Dihedral : 6.326 56.538 1309 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.34 % Favored : 94.40 % Rotamer: Outliers : 4.74 % Allowed : 23.81 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.25), residues: 1160 helix: 0.91 (0.26), residues: 435 sheet: -0.35 (0.34), residues: 228 loop : -1.40 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 241 HIS 0.019 0.002 HIS R 44 PHE 0.018 0.002 PHE N 108 TYR 0.025 0.002 TYR R 145 ARG 0.012 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8034 (mtp85) REVERT: P 21 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6840 (t0) REVERT: B 9 GLN cc_start: 0.9517 (mp10) cc_final: 0.9198 (mp10) REVERT: B 10 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9173 (tp30) REVERT: B 12 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8826 (pp20) REVERT: C 17 GLU cc_start: 0.9216 (tp30) cc_final: 0.8726 (tp30) REVERT: C 20 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8682 (ptpt) REVERT: C 21 MET cc_start: 0.9039 (mmp) cc_final: 0.8780 (mmp) REVERT: C 28 ILE cc_start: 0.8798 (mm) cc_final: 0.8200 (pp) REVERT: C 32 LYS cc_start: 0.8918 (tptp) cc_final: 0.8365 (tppt) REVERT: N 18 LEU cc_start: 0.8601 (mt) cc_final: 0.8154 (mp) REVERT: N 73 ASP cc_start: 0.8311 (t70) cc_final: 0.7622 (t0) REVERT: N 83 MET cc_start: 0.8339 (mtt) cc_final: 0.8017 (mtt) REVERT: R 39 TYR cc_start: 0.9001 (t80) cc_final: 0.8480 (t80) REVERT: R 127 GLU cc_start: 0.8622 (pm20) cc_final: 0.8400 (pm20) REVERT: R 136 LYS cc_start: 0.9211 (mmmm) cc_final: 0.9002 (mtpp) REVERT: R 245 GLU cc_start: 0.8628 (tp30) cc_final: 0.8406 (tp30) REVERT: R 405 LYS cc_start: 0.9245 (mmpt) cc_final: 0.8816 (mmmt) outliers start: 44 outliers final: 24 residues processed: 162 average time/residue: 1.2320 time to fit residues: 213.0175 Evaluate side-chains 158 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 215 TRP Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 416 HIS Chi-restraints excluded: chain R residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 13 GLN B 16 ASN B 88 ASN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9272 Z= 0.199 Angle : 0.643 9.566 12583 Z= 0.322 Chirality : 0.041 0.230 1412 Planarity : 0.004 0.056 1610 Dihedral : 5.788 55.082 1305 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 2.80 % Allowed : 27.05 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.25), residues: 1160 helix: 1.14 (0.26), residues: 444 sheet: -0.11 (0.34), residues: 220 loop : -1.22 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 115 HIS 0.021 0.001 HIS R 44 PHE 0.009 0.001 PHE P 6 TYR 0.019 0.001 TYR R 145 ARG 0.011 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8042 (mtp85) REVERT: A 292 ASN cc_start: 0.9006 (t0) cc_final: 0.8762 (t0) REVERT: B 9 GLN cc_start: 0.9527 (mp10) cc_final: 0.9218 (mp10) REVERT: B 12 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8812 (pp20) REVERT: B 260 GLU cc_start: 0.8642 (pt0) cc_final: 0.8056 (tt0) REVERT: B 275 SER cc_start: 0.8371 (t) cc_final: 0.8092 (m) REVERT: C 17 GLU cc_start: 0.9186 (tp30) cc_final: 0.8681 (tp30) REVERT: C 20 LYS cc_start: 0.9002 (ptpt) cc_final: 0.8704 (ptpt) REVERT: C 28 ILE cc_start: 0.8848 (mm) cc_final: 0.8372 (pp) REVERT: C 32 LYS cc_start: 0.8935 (tptp) cc_final: 0.8320 (tppt) REVERT: C 46 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8814 (pptt) REVERT: N 18 LEU cc_start: 0.8445 (mt) cc_final: 0.8173 (mp) REVERT: N 73 ASP cc_start: 0.8296 (t70) cc_final: 0.7632 (t0) REVERT: R 39 TYR cc_start: 0.8947 (t80) cc_final: 0.8427 (t80) REVERT: R 115 TRP cc_start: 0.7168 (p-90) cc_final: 0.6936 (p-90) REVERT: R 136 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8985 (mtpp) REVERT: R 137 MET cc_start: 0.8508 (ttp) cc_final: 0.8307 (ttm) REVERT: R 328 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (tp) outliers start: 26 outliers final: 11 residues processed: 160 average time/residue: 1.1749 time to fit residues: 201.1878 Evaluate side-chains 149 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 chunk 109 optimal weight: 0.0050 chunk 68 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.1492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 9272 Z= 0.187 Angle : 0.646 11.571 12583 Z= 0.320 Chirality : 0.040 0.213 1412 Planarity : 0.004 0.055 1610 Dihedral : 5.238 50.102 1303 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.43 % Rotamer: Outliers : 2.59 % Allowed : 28.45 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.10 (0.25), residues: 1160 helix: 1.24 (0.26), residues: 447 sheet: -0.15 (0.34), residues: 213 loop : -1.22 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.018 0.001 HIS R 44 PHE 0.016 0.001 PHE R 33 TYR 0.018 0.001 TYR R 145 ARG 0.011 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8955 (t0) cc_final: 0.8693 (t0) REVERT: P 21 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.6037 (t0) REVERT: B 9 GLN cc_start: 0.9568 (mp10) cc_final: 0.9273 (mp10) REVERT: B 12 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8817 (pp20) REVERT: B 260 GLU cc_start: 0.8515 (pt0) cc_final: 0.7983 (tt0) REVERT: B 262 MET cc_start: 0.7884 (tpp) cc_final: 0.7532 (tpp) REVERT: B 275 SER cc_start: 0.8240 (t) cc_final: 0.7995 (m) REVERT: C 17 GLU cc_start: 0.9259 (tp30) cc_final: 0.8430 (tp30) REVERT: C 20 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8682 (pttt) REVERT: C 21 MET cc_start: 0.9000 (mmp) cc_final: 0.8727 (mmp) REVERT: C 28 ILE cc_start: 0.8887 (mm) cc_final: 0.8566 (pp) REVERT: C 46 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8663 (pptt) REVERT: N 18 LEU cc_start: 0.8464 (mt) cc_final: 0.8213 (mt) REVERT: N 73 ASP cc_start: 0.8295 (t70) cc_final: 0.7679 (t0) REVERT: R 39 TYR cc_start: 0.8939 (t80) cc_final: 0.8390 (t80) REVERT: R 136 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8999 (mtpp) REVERT: R 137 MET cc_start: 0.8480 (ttp) cc_final: 0.8264 (ttm) REVERT: R 293 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: R 328 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8628 (tp) REVERT: R 385 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8441 (m-30) outliers start: 24 outliers final: 8 residues processed: 164 average time/residue: 1.1558 time to fit residues: 203.2512 Evaluate side-chains 155 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 293 GLN Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9272 Z= 0.212 Angle : 0.671 11.374 12583 Z= 0.333 Chirality : 0.042 0.214 1412 Planarity : 0.004 0.054 1610 Dihedral : 5.150 48.325 1302 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 2.05 % Allowed : 30.17 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.02 (0.25), residues: 1160 helix: 1.25 (0.26), residues: 449 sheet: -0.05 (0.34), residues: 211 loop : -1.15 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 115 HIS 0.014 0.001 HIS R 45 PHE 0.025 0.001 PHE P 22 TYR 0.018 0.001 TYR R 145 ARG 0.013 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8990 (t0) cc_final: 0.8732 (t0) REVERT: P 21 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.5803 (t0) REVERT: B 9 GLN cc_start: 0.9558 (mp10) cc_final: 0.9321 (mp10) REVERT: B 12 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8837 (tm-30) REVERT: B 260 GLU cc_start: 0.8534 (pt0) cc_final: 0.7980 (tt0) REVERT: B 262 MET cc_start: 0.7872 (tpp) cc_final: 0.7496 (tpp) REVERT: B 275 SER cc_start: 0.8293 (t) cc_final: 0.8022 (m) REVERT: C 17 GLU cc_start: 0.9208 (tp30) cc_final: 0.8310 (tp30) REVERT: C 20 LYS cc_start: 0.8975 (ptpt) cc_final: 0.8647 (pttt) REVERT: C 21 MET cc_start: 0.8987 (mmp) cc_final: 0.8723 (mmp) REVERT: N 73 ASP cc_start: 0.8328 (t70) cc_final: 0.7724 (t0) REVERT: N 82 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7570 (tm-30) REVERT: R 39 TYR cc_start: 0.8960 (t80) cc_final: 0.8325 (t80) REVERT: R 65 TYR cc_start: 0.7587 (p90) cc_final: 0.7188 (p90) REVERT: R 115 TRP cc_start: 0.7072 (p-90) cc_final: 0.6729 (p-90) REVERT: R 136 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8990 (mtpp) REVERT: R 137 MET cc_start: 0.8512 (ttp) cc_final: 0.8304 (ttm) REVERT: R 215 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.8060 (p-90) REVERT: R 328 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8683 (tp) REVERT: R 385 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8397 (m-30) outliers start: 19 outliers final: 9 residues processed: 154 average time/residue: 1.2291 time to fit residues: 202.7128 Evaluate side-chains 151 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 215 TRP Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9272 Z= 0.250 Angle : 0.706 12.730 12583 Z= 0.348 Chirality : 0.042 0.210 1412 Planarity : 0.004 0.059 1610 Dihedral : 5.119 48.003 1300 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.40 % Favored : 95.26 % Rotamer: Outliers : 1.83 % Allowed : 30.82 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1160 helix: 1.27 (0.26), residues: 452 sheet: 0.03 (0.34), residues: 212 loop : -1.15 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 115 HIS 0.010 0.001 HIS R 45 PHE 0.023 0.001 PHE P 22 TYR 0.019 0.001 TYR R 145 ARG 0.014 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.9046 (t0) cc_final: 0.8821 (t0) REVERT: P 21 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6441 (t0) REVERT: B 9 GLN cc_start: 0.9550 (mp10) cc_final: 0.9302 (mp10) REVERT: B 12 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8804 (tm-30) REVERT: B 260 GLU cc_start: 0.8582 (pt0) cc_final: 0.8010 (tt0) REVERT: B 262 MET cc_start: 0.7847 (tpp) cc_final: 0.7447 (tpp) REVERT: B 275 SER cc_start: 0.8356 (t) cc_final: 0.8112 (p) REVERT: C 17 GLU cc_start: 0.9189 (tp30) cc_final: 0.8571 (tp30) REVERT: C 21 MET cc_start: 0.8993 (mmp) cc_final: 0.8766 (mmp) REVERT: N 73 ASP cc_start: 0.8317 (t70) cc_final: 0.7674 (t0) REVERT: N 82 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7589 (tm-30) REVERT: R 38 LEU cc_start: 0.9747 (mm) cc_final: 0.9543 (tm) REVERT: R 39 TYR cc_start: 0.9036 (t80) cc_final: 0.8525 (t80) REVERT: R 115 TRP cc_start: 0.6910 (p-90) cc_final: 0.6556 (p-90) REVERT: R 136 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8973 (mtpp) REVERT: R 137 MET cc_start: 0.8537 (ttp) cc_final: 0.8331 (ttm) REVERT: R 215 TRP cc_start: 0.8335 (t60) cc_final: 0.8017 (p-90) REVERT: R 385 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8380 (m-30) outliers start: 17 outliers final: 10 residues processed: 147 average time/residue: 1.2300 time to fit residues: 193.2535 Evaluate side-chains 150 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9272 Z= 0.242 Angle : 0.719 12.952 12583 Z= 0.358 Chirality : 0.042 0.210 1412 Planarity : 0.004 0.064 1610 Dihedral : 5.138 47.839 1300 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.51 % Allowed : 31.68 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.10 (0.25), residues: 1160 helix: 1.30 (0.26), residues: 452 sheet: 0.03 (0.34), residues: 213 loop : -1.07 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 36 HIS 0.007 0.001 HIS R 45 PHE 0.020 0.001 PHE P 22 TYR 0.019 0.001 TYR R 145 ARG 0.014 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.9057 (t0) cc_final: 0.8829 (t0) REVERT: A 294 GLN cc_start: 0.8378 (tm130) cc_final: 0.8108 (tm-30) REVERT: P 21 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7088 (t0) REVERT: B 9 GLN cc_start: 0.9565 (mp10) cc_final: 0.9331 (mp10) REVERT: B 12 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 260 GLU cc_start: 0.8538 (pt0) cc_final: 0.7986 (tt0) REVERT: B 262 MET cc_start: 0.7783 (tpp) cc_final: 0.7378 (tpp) REVERT: B 275 SER cc_start: 0.8355 (t) cc_final: 0.8110 (p) REVERT: C 17 GLU cc_start: 0.9171 (tp30) cc_final: 0.8564 (tp30) REVERT: C 21 MET cc_start: 0.9016 (mmp) cc_final: 0.8771 (mmp) REVERT: N 73 ASP cc_start: 0.8300 (t70) cc_final: 0.7648 (t0) REVERT: N 82 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7634 (tm-30) REVERT: R 38 LEU cc_start: 0.9736 (mm) cc_final: 0.9534 (tm) REVERT: R 39 TYR cc_start: 0.9082 (t80) cc_final: 0.8511 (t80) REVERT: R 65 TYR cc_start: 0.7754 (p90) cc_final: 0.7414 (p90) REVERT: R 115 TRP cc_start: 0.6959 (p-90) cc_final: 0.6593 (p-90) REVERT: R 136 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8968 (mtpp) REVERT: R 137 MET cc_start: 0.8538 (ttp) cc_final: 0.8332 (ttm) REVERT: R 215 TRP cc_start: 0.8320 (t60) cc_final: 0.8014 (p-90) REVERT: R 385 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8392 (m-30) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 1.2287 time to fit residues: 195.9359 Evaluate side-chains 151 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 67 CYS Chi-restraints excluded: chain R residue 344 LYS Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.2466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.073241 restraints weight = 18172.133| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.61 r_work: 0.2968 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9272 Z= 0.180 Angle : 0.693 11.041 12583 Z= 0.343 Chirality : 0.041 0.203 1412 Planarity : 0.004 0.062 1610 Dihedral : 4.942 48.610 1300 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.97 % Favored : 95.69 % Rotamer: Outliers : 1.51 % Allowed : 31.90 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.25), residues: 1160 helix: 1.35 (0.26), residues: 449 sheet: 0.07 (0.34), residues: 212 loop : -1.05 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 115 HIS 0.010 0.001 HIS R 45 PHE 0.019 0.001 PHE P 22 TYR 0.016 0.001 TYR R 145 ARG 0.014 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.44 seconds wall clock time: 74 minutes 40.10 seconds (4480.10 seconds total)