Starting phenix.real_space_refine on Thu Mar 14 18:22:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e3y_8978/03_2024/6e3y_8978_updated.pdb" } resolution = 3.3 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. 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 68 5.16 5 C 6023 2.51 5 N 1638 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 18": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 119": "NH1" <-> "NH2" Residue "R ARG 274": "NH1" <-> "NH2" Residue "R ARG 314": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9434 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 240 Unusual residues: {'NH2': 1} Classifications: {'peptide': 34, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 32} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1578 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2545 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2813 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 925 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} 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: 6.25, per 1000 atoms: 0.66 Number of scatterers: 9434 At special positions: 0 Unit cell: (84.8, 166.42, 98.58, 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 68 16.00 O 1705 8.00 N 1638 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " 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: 3.47 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... Number of C-beta restraints generated: 2250 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 11 sheets defined 38.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'P' and resid 8 through 19 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 'A' and resid 16 through 39 removed outlier: 3.661A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.549A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.680A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 34 through 53 Processing helix chain 'R' and resid 125 through 129 removed outlier: 3.586A pdb=" N VAL R 129 " --> pdb=" O THR R 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 125 through 129' Processing helix chain 'R' and resid 131 through 166 removed outlier: 3.558A pdb=" N ASN R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 197 removed outlier: 3.825A pdb=" N THR R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 241 removed outlier: 3.788A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.546A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 283 No H-bonds generated for 'chain 'R' and resid 281 through 283' Processing helix chain 'R' and resid 291 through 320 removed outlier: 4.530A pdb=" N GLY R 296 " --> pdb=" O ILE R 293 " (cutoff:3.500A) Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 349 No H-bonds generated for 'chain 'R' and resid 347 through 349' Processing helix chain 'R' and resid 364 through 374 Processing helix chain 'R' and resid 376 through 381 Processing helix chain 'R' and resid 389 through 398 removed outlier: 3.638A pdb=" N ILE R 394 " --> pdb=" O GLU R 390 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG R 397 " --> pdb=" O ALA R 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.895A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 59 through 80 removed outlier: 5.024A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 119 through 142 Proline residue: E 126 - end of helix Processing sheet with id= A, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.581A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.523A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 286 through 291 removed outlier: 4.125A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.158A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.803A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.825A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.863A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.735A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.583A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.751A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 82 through 87 413 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3015 1.34 - 1.46: 2373 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 9648 Sorted by residual: bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.60e-02 3.91e+03 5.12e+00 bond pdb=" CB THR E 130 " pdb=" CG2 THR E 130 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.91e+00 bond pdb=" C PHE R 262 " pdb=" N PRO R 263 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.08e+00 bond pdb=" CB VAL B 71 " pdb=" CG2 VAL B 71 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.03e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.31: 216 106.31 - 113.26: 5247 113.26 - 120.21: 3627 120.21 - 127.16: 3884 127.16 - 134.11: 121 Bond angle restraints: 13095 Sorted by residual: angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.74e+01 angle pdb=" C LEU R 276 " pdb=" N TYR R 277 " pdb=" CA TYR R 277 " ideal model delta sigma weight residual 122.44 117.30 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" N TYR R 277 " pdb=" CA TYR R 277 " pdb=" C TYR R 277 " ideal model delta sigma weight residual 111.02 117.01 -5.99 1.52e+00 4.33e-01 1.56e+01 angle pdb=" N PHE R 262 " pdb=" CA PHE R 262 " pdb=" C PHE R 262 " ideal model delta sigma weight residual 109.81 118.29 -8.48 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 ... (remaining 13090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5377 15.10 - 30.21: 228 30.21 - 45.31: 60 45.31 - 60.41: 8 60.41 - 75.52: 6 Dihedral angle restraints: 5679 sinusoidal: 2206 harmonic: 3473 Sorted by residual: dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 136.24 -43.24 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 128.07 -35.07 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1151 0.067 - 0.134: 282 0.134 - 0.201: 34 0.201 - 0.269: 4 0.269 - 0.336: 1 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CB ILE R 352 " pdb=" CA ILE R 352 " pdb=" CG1 ILE R 352 " pdb=" CG2 ILE R 352 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL R 78 " pdb=" N VAL R 78 " pdb=" C VAL R 78 " pdb=" CB VAL R 78 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1469 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 293 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ILE R 293 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE R 293 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE R 294 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 266 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C PRO R 266 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO R 266 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA R 267 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 352 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO R 353 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 353 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 353 " 0.041 5.00e-02 4.00e+02 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2646 2.81 - 3.33: 8364 3.33 - 3.85: 15970 3.85 - 4.38: 17801 4.38 - 4.90: 31204 Nonbonded interactions: 75985 Sorted by model distance: nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.290 2.440 nonbonded pdb=" O HIS P 10 " pdb=" OG SER R 286 " model vdw 2.296 2.440 nonbonded pdb=" O PRO A 313 " pdb=" NH1 ARG A 317 " model vdw 2.322 2.520 nonbonded pdb=" O GLY P 33 " pdb=" NE1 TRP R 121 " model vdw 2.332 2.520 ... (remaining 75980 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 1.740 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.330 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.007 0.066 9648 Z= 0.452 Angle : 1.004 11.253 13095 Z= 0.572 Chirality : 0.058 0.336 1472 Planarity : 0.008 0.074 1657 Dihedral : 9.693 75.517 3402 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.02 (0.20), residues: 1160 helix: -2.15 (0.19), residues: 457 sheet: -1.04 (0.31), residues: 229 loop : -2.17 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP R 229 HIS 0.013 0.003 HIS R 374 PHE 0.037 0.003 PHE R 163 TYR 0.020 0.003 TYR N 94 ARG 0.009 0.001 ARG A 317 *********************** 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 250 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.152 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9207 (t0) cc_final: 0.8949 (t0) REVERT: N 34 MET cc_start: 0.8439 (mtp) cc_final: 0.8185 (mtp) REVERT: N 65 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8701 (mtmt) REVERT: N 82 GLN cc_start: 0.8305 (tp40) cc_final: 0.7989 (tm-30) REVERT: N 122 THR cc_start: 0.9089 (p) cc_final: 0.8878 (p) REVERT: N 125 THR cc_start: 0.9207 (m) cc_final: 0.8972 (p) REVERT: A 229 ASP cc_start: 0.8799 (m-30) cc_final: 0.8199 (t0) REVERT: A 240 ASP cc_start: 0.8843 (m-30) cc_final: 0.8569 (m-30) REVERT: A 271 LYS cc_start: 0.9240 (mmmt) cc_final: 0.9035 (mmtm) REVERT: B 20 ASP cc_start: 0.9514 (m-30) cc_final: 0.9250 (m-30) REVERT: B 44 GLN cc_start: 0.8859 (pm20) cc_final: 0.7961 (pm20) REVERT: B 155 ASN cc_start: 0.8973 (t160) cc_final: 0.8414 (t0) REVERT: B 210 LEU cc_start: 0.9198 (tp) cc_final: 0.8977 (tp) REVERT: B 254 ASP cc_start: 0.8085 (t0) cc_final: 0.7808 (t0) REVERT: B 301 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8290 (mttp) REVERT: R 42 MET cc_start: 0.9294 (mmp) cc_final: 0.8923 (mmp) REVERT: R 96 ASP cc_start: 0.8606 (t0) cc_final: 0.8398 (t0) REVERT: R 99 GLU cc_start: 0.7661 (tp30) cc_final: 0.7269 (tm-30) REVERT: R 178 LYS cc_start: 0.8831 (mttt) cc_final: 0.8624 (mtpp) REVERT: R 280 ASP cc_start: 0.9133 (t0) cc_final: 0.8604 (p0) REVERT: R 332 MET cc_start: 0.7634 (mmm) cc_final: 0.7400 (tmm) REVERT: R 373 MET cc_start: 0.8709 (ttm) cc_final: 0.8400 (tmm) REVERT: E 58 ASP cc_start: 0.9376 (t0) cc_final: 0.9161 (t0) REVERT: E 67 ARG cc_start: 0.8668 (ptt180) cc_final: 0.8301 (ptm160) REVERT: E 76 MET cc_start: 0.9150 (tpp) cc_final: 0.8935 (mmp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3061 time to fit residues: 96.2716 Evaluate side-chains 130 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 HIS A 23 ASN A 278 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN G 18 GLN R 172 GLN R 270 HIS ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9648 Z= 0.190 Angle : 0.608 10.454 13095 Z= 0.322 Chirality : 0.042 0.166 1472 Planarity : 0.005 0.047 1657 Dihedral : 4.673 60.027 1294 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.08 % Allowed : 11.00 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.92 (0.23), residues: 1160 helix: 0.35 (0.23), residues: 459 sheet: -0.64 (0.32), residues: 229 loop : -1.49 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 229 HIS 0.006 0.001 HIS R 374 PHE 0.022 0.001 PHE E 92 TYR 0.020 0.001 TYR A 358 ARG 0.007 0.001 ARG P 18 *********************** 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 168 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.886 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 6 THR cc_start: 0.8969 (p) cc_final: 0.8701 (p) REVERT: P 16 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9189 (mp) REVERT: P 31 ASN cc_start: 0.9227 (t0) cc_final: 0.8985 (t0) REVERT: N 11 LEU cc_start: 0.9171 (tp) cc_final: 0.8876 (mm) REVERT: N 65 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8640 (mtmt) REVERT: N 73 ASP cc_start: 0.7166 (p0) cc_final: 0.6895 (p0) REVERT: N 87 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7828 (mptt) REVERT: N 125 THR cc_start: 0.9203 (m) cc_final: 0.8691 (p) REVERT: B 32 GLN cc_start: 0.8872 (mt0) cc_final: 0.8649 (mt0) REVERT: B 44 GLN cc_start: 0.8564 (pm20) cc_final: 0.7993 (pm20) REVERT: B 215 GLU cc_start: 0.8629 (mp0) cc_final: 0.8429 (mp0) REVERT: B 254 ASP cc_start: 0.8180 (t0) cc_final: 0.7910 (t0) REVERT: B 301 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8180 (mttp) REVERT: R 42 MET cc_start: 0.9305 (mmp) cc_final: 0.8975 (mmp) REVERT: R 96 ASP cc_start: 0.8140 (t0) cc_final: 0.7296 (t0) REVERT: R 99 GLU cc_start: 0.7690 (tp30) cc_final: 0.7456 (mm-30) REVERT: R 280 ASP cc_start: 0.9192 (t0) cc_final: 0.8611 (p0) REVERT: R 332 MET cc_start: 0.7673 (mmm) cc_final: 0.7443 (tmm) REVERT: E 58 ASP cc_start: 0.9362 (t0) cc_final: 0.9150 (t0) REVERT: E 67 ARG cc_start: 0.8608 (ptt180) cc_final: 0.8181 (ptm160) REVERT: E 76 MET cc_start: 0.9209 (tpp) cc_final: 0.8888 (mmp) REVERT: E 83 PHE cc_start: 0.8277 (p90) cc_final: 0.8023 (p90) outliers start: 21 outliers final: 10 residues processed: 160 average time/residue: 0.2700 time to fit residues: 56.6915 Evaluate side-chains 135 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9648 Z= 0.161 Angle : 0.561 11.027 13095 Z= 0.293 Chirality : 0.041 0.166 1472 Planarity : 0.004 0.057 1657 Dihedral : 4.561 53.915 1294 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.68 % Allowed : 13.18 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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 (0.24), residues: 1160 helix: 1.20 (0.24), residues: 457 sheet: -0.56 (0.32), residues: 231 loop : -1.26 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 374 PHE 0.014 0.001 PHE B 199 TYR 0.026 0.001 TYR N 80 ARG 0.009 0.000 ARG P 18 *********************** 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 153 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.255 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9234 (t0) cc_final: 0.8994 (t0) REVERT: N 11 LEU cc_start: 0.9180 (tp) cc_final: 0.8868 (mm) REVERT: N 34 MET cc_start: 0.8487 (mtp) cc_final: 0.8273 (mmm) REVERT: N 73 ASP cc_start: 0.6937 (p0) cc_final: 0.6624 (p0) REVERT: N 87 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7696 (mptt) REVERT: N 125 THR cc_start: 0.9231 (m) cc_final: 0.8653 (p) REVERT: B 44 GLN cc_start: 0.8604 (pm20) cc_final: 0.8028 (pm20) REVERT: B 188 MET cc_start: 0.8640 (mmm) cc_final: 0.8361 (mmm) REVERT: B 254 ASP cc_start: 0.8221 (t0) cc_final: 0.7953 (t0) REVERT: B 301 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8205 (mttp) REVERT: G 32 LYS cc_start: 0.8946 (ptmm) cc_final: 0.8591 (ptmm) REVERT: G 38 MET cc_start: 0.9251 (ttp) cc_final: 0.8627 (ptp) REVERT: R 42 MET cc_start: 0.9288 (mmp) cc_final: 0.8884 (mmp) REVERT: R 99 GLU cc_start: 0.7664 (tp30) cc_final: 0.7445 (tp30) REVERT: R 280 ASP cc_start: 0.9200 (t0) cc_final: 0.8612 (p0) REVERT: R 332 MET cc_start: 0.7727 (mmm) cc_final: 0.7465 (tmm) REVERT: R 373 MET cc_start: 0.8814 (tmm) cc_final: 0.8386 (tmm) REVERT: R 386 PHE cc_start: 0.8481 (m-80) cc_final: 0.8189 (t80) REVERT: E 58 ASP cc_start: 0.9365 (t0) cc_final: 0.9164 (t0) REVERT: E 67 ARG cc_start: 0.8536 (ptt180) cc_final: 0.8092 (ptm160) REVERT: E 83 PHE cc_start: 0.8316 (p90) cc_final: 0.8081 (p90) REVERT: E 91 ARG cc_start: 0.9148 (mtp85) cc_final: 0.8870 (ptp90) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 0.2796 time to fit residues: 53.8601 Evaluate side-chains 133 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 282 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 0.0020 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 54 GLN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9648 Z= 0.145 Angle : 0.544 9.618 13095 Z= 0.285 Chirality : 0.040 0.157 1472 Planarity : 0.003 0.048 1657 Dihedral : 4.363 48.105 1294 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.38 % Allowed : 13.48 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 1.54 (0.25), residues: 457 sheet: -0.36 (0.33), residues: 225 loop : -1.08 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 374 PHE 0.013 0.001 PHE B 199 TYR 0.017 0.001 TYR N 80 ARG 0.010 0.000 ARG P 18 *********************** 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 156 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.118 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 16 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9138 (mp) REVERT: P 31 ASN cc_start: 0.9240 (t0) cc_final: 0.9013 (t0) REVERT: N 11 LEU cc_start: 0.9167 (tp) cc_final: 0.8859 (mm) REVERT: N 84 ASN cc_start: 0.8777 (m-40) cc_final: 0.8552 (m110) REVERT: N 87 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8093 (mptt) REVERT: N 125 THR cc_start: 0.9221 (m) cc_final: 0.8642 (p) REVERT: B 44 GLN cc_start: 0.8595 (pm20) cc_final: 0.8056 (pm20) REVERT: B 188 MET cc_start: 0.8676 (mmm) cc_final: 0.8415 (mmm) REVERT: B 215 GLU cc_start: 0.8099 (mp0) cc_final: 0.7866 (mp0) REVERT: B 254 ASP cc_start: 0.8225 (t0) cc_final: 0.7934 (t0) REVERT: B 301 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8197 (mttp) REVERT: G 21 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8655 (tmm) REVERT: G 32 LYS cc_start: 0.8964 (ptmm) cc_final: 0.8622 (ptmm) REVERT: G 38 MET cc_start: 0.9193 (ttp) cc_final: 0.8713 (ptm) REVERT: R 38 ARG cc_start: 0.9185 (mmt180) cc_final: 0.8903 (tpp80) REVERT: R 42 MET cc_start: 0.9314 (mmp) cc_final: 0.8877 (mmp) REVERT: R 332 MET cc_start: 0.7695 (mmm) cc_final: 0.7458 (tmm) REVERT: R 373 MET cc_start: 0.8921 (tmm) cc_final: 0.8495 (tmm) REVERT: R 386 PHE cc_start: 0.8426 (m-80) cc_final: 0.8194 (t80) REVERT: E 67 ARG cc_start: 0.8450 (ptt180) cc_final: 0.7959 (ptm160) REVERT: E 76 MET cc_start: 0.9207 (ttm) cc_final: 0.8771 (ttt) REVERT: E 83 PHE cc_start: 0.8303 (p90) cc_final: 0.8046 (p90) outliers start: 24 outliers final: 12 residues processed: 149 average time/residue: 0.2693 time to fit residues: 53.0942 Evaluate side-chains 137 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 198 VAL Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain E residue 45 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9648 Z= 0.468 Angle : 0.718 8.286 13095 Z= 0.377 Chirality : 0.045 0.158 1472 Planarity : 0.004 0.036 1657 Dihedral : 4.698 42.286 1294 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.36 % Allowed : 12.88 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.18 (0.24), residues: 1160 helix: 1.45 (0.25), residues: 468 sheet: -0.21 (0.33), residues: 226 loop : -1.05 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.021 0.002 HIS A 220 PHE 0.015 0.002 PHE B 199 TYR 0.030 0.002 TYR N 80 ARG 0.009 0.001 ARG P 18 *********************** 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 170 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 31 ASN cc_start: 0.9253 (t0) cc_final: 0.9030 (t0) REVERT: N 11 LEU cc_start: 0.9225 (tp) cc_final: 0.8877 (mm) REVERT: N 69 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8514 (t) REVERT: N 73 ASP cc_start: 0.7186 (p0) cc_final: 0.6877 (p0) REVERT: N 83 MET cc_start: 0.7994 (mmm) cc_final: 0.7749 (mmm) REVERT: N 125 THR cc_start: 0.9239 (m) cc_final: 0.8718 (p) REVERT: A 229 ASP cc_start: 0.8841 (m-30) cc_final: 0.8187 (t0) REVERT: A 240 ASP cc_start: 0.8790 (m-30) cc_final: 0.8471 (m-30) REVERT: B 44 GLN cc_start: 0.8649 (pm20) cc_final: 0.8047 (pm20) REVERT: B 254 ASP cc_start: 0.8279 (t0) cc_final: 0.8035 (t0) REVERT: B 301 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8326 (mmtp) REVERT: G 38 MET cc_start: 0.9226 (ttp) cc_final: 0.8734 (ptm) REVERT: R 38 ARG cc_start: 0.9214 (mmt180) cc_final: 0.8949 (tpp80) REVERT: R 42 MET cc_start: 0.9303 (mmp) cc_final: 0.9015 (mmp) REVERT: R 99 GLU cc_start: 0.7578 (tp30) cc_final: 0.7335 (tp30) REVERT: R 332 MET cc_start: 0.7846 (mmm) cc_final: 0.7591 (tmm) REVERT: R 373 MET cc_start: 0.8903 (tmm) cc_final: 0.8348 (tmm) REVERT: E 51 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7331 (p) REVERT: E 67 ARG cc_start: 0.8449 (ptt180) cc_final: 0.7927 (ptm160) REVERT: E 76 MET cc_start: 0.9161 (ttm) cc_final: 0.8875 (ttm) REVERT: E 91 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8919 (ptp90) outliers start: 44 outliers final: 33 residues processed: 153 average time/residue: 0.2776 time to fit residues: 55.5310 Evaluate side-chains 150 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 100 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN R 50 GLN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9648 Z= 0.205 Angle : 0.586 9.287 13095 Z= 0.305 Chirality : 0.041 0.157 1472 Planarity : 0.003 0.033 1657 Dihedral : 4.547 37.650 1294 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.18 % Allowed : 15.66 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.24 (0.24), residues: 1160 helix: 1.59 (0.25), residues: 466 sheet: -0.29 (0.32), residues: 226 loop : -1.06 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 99 HIS 0.005 0.001 HIS R 374 PHE 0.023 0.001 PHE E 83 TYR 0.012 0.001 TYR B 105 ARG 0.007 0.000 ARG P 18 *********************** 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 153 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.128 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: symmetry clash REVERT: P 18 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: N 11 LEU cc_start: 0.9200 (tp) cc_final: 0.8856 (mm) REVERT: N 69 THR cc_start: 0.8743 (m) cc_final: 0.8384 (t) REVERT: N 73 ASP cc_start: 0.7197 (p0) cc_final: 0.5721 (p0) REVERT: N 125 THR cc_start: 0.9235 (m) cc_final: 0.8659 (p) REVERT: A 27 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 229 ASP cc_start: 0.8839 (m-30) cc_final: 0.8332 (t70) REVERT: A 240 ASP cc_start: 0.8775 (m-30) cc_final: 0.8445 (m-30) REVERT: A 386 MET cc_start: 0.8606 (ttm) cc_final: 0.8215 (tmm) REVERT: B 44 GLN cc_start: 0.8637 (pm20) cc_final: 0.7976 (pm20) REVERT: B 217 MET cc_start: 0.8606 (pmm) cc_final: 0.8063 (pmm) REVERT: B 254 ASP cc_start: 0.8224 (t0) cc_final: 0.7982 (t0) REVERT: B 266 HIS cc_start: 0.8780 (t-90) cc_final: 0.8539 (t-90) REVERT: B 301 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8375 (mmtp) REVERT: G 32 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8716 (ptmm) REVERT: G 38 MET cc_start: 0.9148 (ttp) cc_final: 0.8706 (ptm) REVERT: R 38 ARG cc_start: 0.9195 (mmt180) cc_final: 0.8884 (tpp80) REVERT: R 42 MET cc_start: 0.9289 (mmp) cc_final: 0.8988 (mmp) REVERT: R 99 GLU cc_start: 0.7391 (tp30) cc_final: 0.7171 (tp30) REVERT: R 332 MET cc_start: 0.7760 (mmm) cc_final: 0.7499 (tmm) REVERT: R 373 MET cc_start: 0.8848 (tmm) cc_final: 0.8295 (tmm) REVERT: E 51 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7285 (p) REVERT: E 58 ASP cc_start: 0.9170 (t0) cc_final: 0.8903 (p0) REVERT: E 61 ARG cc_start: 0.8776 (tpt90) cc_final: 0.8457 (tpt170) REVERT: E 67 ARG cc_start: 0.8408 (ptt180) cc_final: 0.7887 (ptm160) REVERT: E 76 MET cc_start: 0.9147 (ttm) cc_final: 0.8881 (ttm) REVERT: E 91 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8962 (ptp-110) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.2815 time to fit residues: 53.6513 Evaluate side-chains 139 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9648 Z= 0.255 Angle : 0.605 8.869 13095 Z= 0.316 Chirality : 0.042 0.235 1472 Planarity : 0.003 0.032 1657 Dihedral : 4.494 35.778 1294 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.28 % Allowed : 15.26 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.27 (0.25), residues: 1160 helix: 1.58 (0.25), residues: 469 sheet: -0.28 (0.32), residues: 231 loop : -1.03 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.005 0.001 HIS R 374 PHE 0.029 0.001 PHE E 83 TYR 0.012 0.001 TYR B 105 ARG 0.006 0.000 ARG P 18 *********************** 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 148 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: N 11 LEU cc_start: 0.9213 (tp) cc_final: 0.8873 (mm) REVERT: N 87 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8115 (mptt) REVERT: N 125 THR cc_start: 0.9244 (m) cc_final: 0.8677 (p) REVERT: A 229 ASP cc_start: 0.8850 (m-30) cc_final: 0.8328 (t70) REVERT: A 240 ASP cc_start: 0.8763 (m-30) cc_final: 0.8429 (m-30) REVERT: B 44 GLN cc_start: 0.8650 (pm20) cc_final: 0.7991 (pm20) REVERT: B 217 MET cc_start: 0.8598 (pmm) cc_final: 0.8050 (pmm) REVERT: B 226 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8017 (mm-30) REVERT: B 254 ASP cc_start: 0.8242 (t0) cc_final: 0.7999 (t0) REVERT: B 301 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8354 (mmtp) REVERT: G 32 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8737 (ptmm) REVERT: G 38 MET cc_start: 0.9158 (ttp) cc_final: 0.8725 (ptm) REVERT: R 38 ARG cc_start: 0.9198 (mmt180) cc_final: 0.8901 (tpp80) REVERT: R 42 MET cc_start: 0.9285 (mmp) cc_final: 0.9004 (mmp) REVERT: R 332 MET cc_start: 0.7773 (mmm) cc_final: 0.7508 (tmm) REVERT: R 373 MET cc_start: 0.8869 (tmm) cc_final: 0.8327 (tmm) REVERT: E 51 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7787 (p) REVERT: E 53 GLU cc_start: 0.8845 (tp30) cc_final: 0.8639 (tp30) REVERT: E 58 ASP cc_start: 0.9188 (t0) cc_final: 0.8915 (p0) REVERT: E 64 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7290 (ppt170) REVERT: E 67 ARG cc_start: 0.8397 (ptt180) cc_final: 0.7905 (ptm160) REVERT: E 76 MET cc_start: 0.9124 (ttm) cc_final: 0.8817 (ttm) REVERT: E 91 ARG cc_start: 0.9194 (mtp85) cc_final: 0.8967 (ptp-110) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.2751 time to fit residues: 50.9276 Evaluate side-chains 141 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9648 Z= 0.246 Angle : 0.628 9.032 13095 Z= 0.328 Chirality : 0.042 0.160 1472 Planarity : 0.003 0.031 1657 Dihedral : 4.516 36.863 1294 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.58 % Allowed : 16.15 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 1160 helix: 1.59 (0.25), residues: 469 sheet: -0.34 (0.32), residues: 231 loop : -0.97 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.005 0.001 HIS R 374 PHE 0.028 0.001 PHE E 83 TYR 0.013 0.001 TYR N 80 ARG 0.006 0.000 ARG P 18 *********************** 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 152 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8104 (ttp80) REVERT: N 11 LEU cc_start: 0.9209 (tp) cc_final: 0.8868 (mm) REVERT: N 19 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8656 (tpp80) REVERT: N 87 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8092 (mptt) REVERT: N 125 THR cc_start: 0.9243 (m) cc_final: 0.8672 (p) REVERT: A 229 ASP cc_start: 0.8856 (m-30) cc_final: 0.8319 (t70) REVERT: A 240 ASP cc_start: 0.8755 (m-30) cc_final: 0.8414 (m-30) REVERT: B 44 GLN cc_start: 0.8677 (pm20) cc_final: 0.7997 (pm20) REVERT: B 217 MET cc_start: 0.8637 (pmm) cc_final: 0.8089 (pmm) REVERT: B 226 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8136 (mm-30) REVERT: B 254 ASP cc_start: 0.8236 (t0) cc_final: 0.7994 (t0) REVERT: B 301 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8400 (mmtp) REVERT: G 32 LYS cc_start: 0.9049 (ptmm) cc_final: 0.8754 (ptmm) REVERT: G 38 MET cc_start: 0.9147 (ttp) cc_final: 0.8726 (ptm) REVERT: R 38 ARG cc_start: 0.9197 (mmt180) cc_final: 0.8898 (tpp80) REVERT: R 42 MET cc_start: 0.9271 (mmp) cc_final: 0.8996 (mmp) REVERT: R 99 GLU cc_start: 0.7116 (tp30) cc_final: 0.6914 (tp30) REVERT: R 113 ARG cc_start: 0.8953 (mpt180) cc_final: 0.8638 (mpt180) REVERT: R 332 MET cc_start: 0.7772 (mmm) cc_final: 0.7509 (tmm) REVERT: R 373 MET cc_start: 0.8877 (tmm) cc_final: 0.8328 (tmm) REVERT: E 51 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7762 (p) REVERT: E 53 GLU cc_start: 0.8840 (tp30) cc_final: 0.8628 (tp30) REVERT: E 58 ASP cc_start: 0.9199 (t0) cc_final: 0.8923 (p0) REVERT: E 64 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7305 (ppt170) REVERT: E 67 ARG cc_start: 0.8406 (ptt180) cc_final: 0.7998 (ptm160) REVERT: E 76 MET cc_start: 0.9119 (ttm) cc_final: 0.8807 (ttm) REVERT: E 91 ARG cc_start: 0.9196 (mtp85) cc_final: 0.8962 (ptp-110) outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 0.2771 time to fit residues: 52.4695 Evaluate side-chains 145 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9648 Z= 0.212 Angle : 0.652 18.027 13095 Z= 0.339 Chirality : 0.041 0.195 1472 Planarity : 0.004 0.038 1657 Dihedral : 4.473 36.294 1294 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 16.55 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.33 (0.25), residues: 1160 helix: 1.66 (0.25), residues: 467 sheet: -0.33 (0.32), residues: 231 loop : -0.95 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 229 HIS 0.004 0.001 HIS R 374 PHE 0.026 0.001 PHE E 83 TYR 0.010 0.001 TYR N 80 ARG 0.006 0.000 ARG P 18 *********************** 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 148 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 LEU cc_start: 0.9194 (tp) cc_final: 0.8860 (mm) REVERT: N 19 ARG cc_start: 0.8870 (tpp80) cc_final: 0.8664 (tpp80) REVERT: N 73 ASP cc_start: 0.7259 (p0) cc_final: 0.5885 (p0) REVERT: N 87 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8228 (mmtt) REVERT: N 125 THR cc_start: 0.9245 (m) cc_final: 0.8674 (p) REVERT: A 229 ASP cc_start: 0.8843 (m-30) cc_final: 0.8308 (t70) REVERT: A 240 ASP cc_start: 0.8758 (m-30) cc_final: 0.8409 (m-30) REVERT: B 44 GLN cc_start: 0.8668 (pm20) cc_final: 0.7978 (pm20) REVERT: B 217 MET cc_start: 0.8650 (pmm) cc_final: 0.8089 (pmm) REVERT: B 226 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8121 (mm-30) REVERT: B 254 ASP cc_start: 0.8237 (t0) cc_final: 0.7996 (t0) REVERT: B 301 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8360 (mttp) REVERT: G 32 LYS cc_start: 0.9036 (ptmm) cc_final: 0.8739 (ptmm) REVERT: G 38 MET cc_start: 0.9126 (ttp) cc_final: 0.8716 (ptm) REVERT: R 38 ARG cc_start: 0.9184 (mmt180) cc_final: 0.8930 (tpp80) REVERT: R 42 MET cc_start: 0.9271 (mmp) cc_final: 0.8998 (mmp) REVERT: R 99 GLU cc_start: 0.7159 (tp30) cc_final: 0.6933 (tp30) REVERT: R 113 ARG cc_start: 0.8989 (mpt180) cc_final: 0.8673 (mpt180) REVERT: R 332 MET cc_start: 0.7759 (mmm) cc_final: 0.7502 (tmm) REVERT: R 373 MET cc_start: 0.8874 (tmm) cc_final: 0.8314 (tmm) REVERT: E 51 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7100 (p) REVERT: E 58 ASP cc_start: 0.9193 (t0) cc_final: 0.8891 (p0) REVERT: E 67 ARG cc_start: 0.8314 (ptt180) cc_final: 0.7850 (ptm160) REVERT: E 76 MET cc_start: 0.9095 (ttm) cc_final: 0.8890 (ttm) REVERT: E 91 ARG cc_start: 0.9195 (mtp85) cc_final: 0.8963 (ptp-110) REVERT: E 99 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.8151 (tmm-80) outliers start: 22 outliers final: 18 residues processed: 142 average time/residue: 0.2803 time to fit residues: 52.5772 Evaluate side-chains 142 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0980 chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9648 Z= 0.159 Angle : 0.599 8.892 13095 Z= 0.311 Chirality : 0.041 0.146 1472 Planarity : 0.003 0.033 1657 Dihedral : 4.305 35.069 1294 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.18 % Allowed : 16.75 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 1.74 (0.25), residues: 467 sheet: -0.17 (0.33), residues: 227 loop : -0.86 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 229 HIS 0.004 0.001 HIS R 374 PHE 0.025 0.001 PHE E 83 TYR 0.010 0.001 TYR N 80 ARG 0.006 0.000 ARG P 18 ********************** 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 147 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 LEU cc_start: 0.9164 (tp) cc_final: 0.8833 (mm) REVERT: N 19 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8722 (tpp80) REVERT: N 65 LYS cc_start: 0.8976 (mttm) cc_final: 0.8165 (mtmt) REVERT: N 76 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (tmtt) REVERT: N 80 TYR cc_start: 0.8580 (m-80) cc_final: 0.8318 (m-10) REVERT: N 87 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8237 (mmtt) REVERT: N 125 THR cc_start: 0.9239 (m) cc_final: 0.8674 (p) REVERT: A 229 ASP cc_start: 0.8867 (m-30) cc_final: 0.8284 (t70) REVERT: A 240 ASP cc_start: 0.8773 (m-30) cc_final: 0.8395 (m-30) REVERT: B 44 GLN cc_start: 0.8707 (pm20) cc_final: 0.8036 (pm20) REVERT: B 217 MET cc_start: 0.8655 (pmm) cc_final: 0.8094 (pmm) REVERT: B 226 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8147 (mm-30) REVERT: B 254 ASP cc_start: 0.8241 (t0) cc_final: 0.7987 (t0) REVERT: B 301 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8363 (mttp) REVERT: B 312 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8217 (p0) REVERT: G 32 LYS cc_start: 0.9035 (ptmm) cc_final: 0.8752 (ptmm) REVERT: G 38 MET cc_start: 0.9104 (ttp) cc_final: 0.8889 (ptm) REVERT: R 38 ARG cc_start: 0.9160 (mmt180) cc_final: 0.8922 (tpp80) REVERT: R 42 MET cc_start: 0.9244 (mmp) cc_final: 0.8959 (mmp) REVERT: R 99 GLU cc_start: 0.7170 (tp30) cc_final: 0.6961 (tp30) REVERT: R 113 ARG cc_start: 0.9012 (mpt180) cc_final: 0.8680 (mpt180) REVERT: R 332 MET cc_start: 0.7735 (mmm) cc_final: 0.7491 (tmm) REVERT: R 373 MET cc_start: 0.8902 (tmm) cc_final: 0.8346 (tmm) REVERT: E 51 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7639 (p) REVERT: E 58 ASP cc_start: 0.9177 (t0) cc_final: 0.8832 (p0) REVERT: E 67 ARG cc_start: 0.8294 (ptt180) cc_final: 0.7840 (ptm160) REVERT: E 76 MET cc_start: 0.9085 (ttm) cc_final: 0.8863 (ttm) REVERT: E 91 ARG cc_start: 0.9190 (mtp85) cc_final: 0.8956 (ptp-110) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.2659 time to fit residues: 49.5872 Evaluate side-chains 140 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 282 CYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 72 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 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 = 0.3502 r_free = 0.3502 target = 0.069415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053584 restraints weight = 33521.795| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.87 r_work: 0.2957 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9648 Z= 0.212 Angle : 0.615 8.769 13095 Z= 0.320 Chirality : 0.041 0.148 1472 Planarity : 0.003 0.044 1657 Dihedral : 4.258 34.213 1294 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.98 % Allowed : 17.24 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1160 helix: 1.79 (0.25), residues: 464 sheet: -0.16 (0.33), residues: 229 loop : -0.79 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 229 HIS 0.004 0.001 HIS R 374 PHE 0.027 0.001 PHE E 83 TYR 0.009 0.001 TYR N 80 ARG 0.004 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.08 seconds wall clock time: 39 minutes 38.33 seconds (2378.33 seconds total)