Starting phenix.real_space_refine on Thu Feb 15 02:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgp_24453/02_2024/7rgp_24453_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 65 5.16 5 C 6884 2.51 5 N 1853 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10795 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1773 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 240 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2999 Classifications: {'peptide': 378} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 6.23, per 1000 atoms: 0.58 Number of scatterers: 10795 At special positions: 0 Unit cell: (163.904, 123.136, 105.664, 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 65 16.00 O 1993 8.00 N 1853 7.00 C 6884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 4.46 Conformation dependent library (CDL) restraints added in 2.0 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 16 sheets defined 30.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 removed outlier: 3.929A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.781A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.544A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 372 through 389 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.700A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 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 'P' and resid 4 through 28 Processing helix chain 'R' and resid 32 through 51 Processing helix chain 'R' and resid 91 through 94 Processing helix chain 'R' and resid 140 through 165 removed outlier: 4.098A pdb=" N TYR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 205 removed outlier: 3.867A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 242 removed outlier: 4.067A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 256 Processing helix chain 'R' and resid 262 through 291 removed outlier: 3.727A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix removed outlier: 3.691A pdb=" N LYS R 288 " --> pdb=" O TRP R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 337 removed outlier: 4.984A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 4.028A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 355 removed outlier: 4.310A pdb=" N LEU R 354 " --> pdb=" O ALA R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 360 No H-bonds generated for 'chain 'R' and resid 357 through 360' Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.591A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 392 removed outlier: 4.132A pdb=" N LEU R 388 " --> pdb=" O LEU R 384 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 407 through 420 removed outlier: 3.692A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 40 through 45 removed outlier: 6.994A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 244 through 249 removed outlier: 3.624A pdb=" N VAL A 248 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 289 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.066A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.618A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.836A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 201 removed outlier: 6.647A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.840A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.540A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 327 through 330 Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.165A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.389A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 147 Processing sheet with id= N, first strand: chain 'E' and resid 164 through 167 removed outlier: 5.868A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= P, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.050A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1191 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: 2.87 Time building geometry restraints manager: 4.81 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: 3393 1.34 - 1.46: 2264 1.46 - 1.58: 5292 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11039 Sorted by residual: bond pdb=" N VAL R 259 " pdb=" CA VAL R 259 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.66e+00 bond pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.17e-02 7.31e+03 7.75e+00 bond pdb=" N VAL R 319 " pdb=" CA VAL R 319 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.65e+00 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.41e+00 bond pdb=" N ARG G 62 " pdb=" CA ARG G 62 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.82e+00 ... (remaining 11034 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.22: 163 105.22 - 112.51: 5570 112.51 - 119.81: 3852 119.81 - 127.10: 5258 127.10 - 134.39: 140 Bond angle restraints: 14983 Sorted by residual: angle pdb=" N GLU A 15 " pdb=" CA GLU A 15 " pdb=" C GLU A 15 " ideal model delta sigma weight residual 114.12 105.96 8.16 1.39e+00 5.18e-01 3.44e+01 angle pdb=" N GLN A 384 " pdb=" CA GLN A 384 " pdb=" C GLN A 384 " ideal model delta sigma weight residual 111.36 106.30 5.06 1.09e+00 8.42e-01 2.16e+01 angle pdb=" C GLN A 384 " pdb=" CA GLN A 384 " pdb=" CB GLN A 384 " ideal model delta sigma weight residual 110.85 117.46 -6.61 1.70e+00 3.46e-01 1.51e+01 angle pdb=" C VAL A 20 " pdb=" N GLU A 21 " pdb=" CA GLU A 21 " ideal model delta sigma weight residual 120.29 115.41 4.88 1.42e+00 4.96e-01 1.18e+01 angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.14e+01 ... (remaining 14978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5860 17.99 - 35.99: 527 35.99 - 53.98: 88 53.98 - 71.98: 15 71.98 - 89.97: 15 Dihedral angle restraints: 6505 sinusoidal: 2496 harmonic: 4009 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -3.12 -82.88 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -166.54 80.54 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CA PHE A 222 " pdb=" C PHE A 222 " pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1321 0.063 - 0.125: 305 0.125 - 0.188: 37 0.188 - 0.250: 2 0.250 - 0.312: 3 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CB VAL R 259 " pdb=" CA VAL R 259 " pdb=" CG1 VAL R 259 " pdb=" CG2 VAL R 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1665 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 243 " -0.041 2.00e-02 2.50e+03 3.53e-02 3.12e+01 pdb=" CG TRP R 243 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP R 243 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP R 243 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP R 243 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 243 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 243 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 243 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 243 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP R 243 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 236 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 222 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.17e+00 pdb=" CG PHE A 222 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 222 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 222 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 222 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 222 " -0.001 2.00e-02 2.50e+03 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 400 2.70 - 3.25: 11269 3.25 - 3.80: 17690 3.80 - 4.35: 23090 4.35 - 4.90: 37612 Nonbonded interactions: 90061 Sorted by model distance: nonbonded pdb=" O ASP B 76 " pdb=" OD1 ASP B 76 " model vdw 2.145 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.201 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.203 2.440 nonbonded pdb=" O TRP R 203 " pdb=" OG1 THR R 207 " model vdw 2.205 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.205 2.440 ... (remaining 90056 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: 0.010 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.480 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11039 Z= 0.423 Angle : 0.925 10.017 14983 Z= 0.514 Chirality : 0.053 0.312 1668 Planarity : 0.006 0.074 1900 Dihedral : 14.391 89.971 3897 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.88 % Allowed : 1.14 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.81 (0.22), residues: 1346 helix: -1.79 (0.22), residues: 437 sheet: -1.71 (0.27), residues: 331 loop : -1.84 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.004 TRP R 243 HIS 0.008 0.002 HIS A 357 PHE 0.048 0.003 PHE A 222 TYR 0.031 0.002 TYR R 148 ARG 0.019 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 1.336 Fit side-chains REVERT: A 229 ASP cc_start: 0.6787 (p0) cc_final: 0.6395 (p0) REVERT: A 293 LYS cc_start: 0.8029 (mptt) cc_final: 0.7737 (mmtt) outliers start: 10 outliers final: 0 residues processed: 223 average time/residue: 1.2195 time to fit residues: 292.4821 Evaluate side-chains 138 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 20.0000 chunk 101 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN E 174 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11039 Z= 0.226 Angle : 0.690 9.039 14983 Z= 0.354 Chirality : 0.044 0.161 1668 Planarity : 0.005 0.071 1900 Dihedral : 5.997 69.922 1508 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.99 % Allowed : 14.86 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.16 (0.22), residues: 1346 helix: -1.12 (0.23), residues: 434 sheet: -1.30 (0.28), residues: 332 loop : -1.61 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 243 HIS 0.006 0.001 HIS A 220 PHE 0.027 0.002 PHE E 200 TYR 0.033 0.001 TYR R 148 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.244 Fit side-chains REVERT: A 323 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: E 180 MET cc_start: 0.6745 (tmm) cc_final: 0.6447 (tmm) REVERT: N 106 ASP cc_start: 0.5047 (t70) cc_final: 0.4716 (t70) REVERT: R 40 ARG cc_start: 0.5285 (mpt-90) cc_final: 0.4953 (mpt-90) REVERT: R 288 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6319 (ttmt) outliers start: 34 outliers final: 9 residues processed: 193 average time/residue: 0.9446 time to fit residues: 197.2856 Evaluate side-chains 154 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 239 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 174 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11039 Z= 0.195 Angle : 0.629 9.590 14983 Z= 0.323 Chirality : 0.043 0.168 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.612 70.837 1508 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.78 % Allowed : 18.65 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.79 (0.23), residues: 1346 helix: -0.66 (0.24), residues: 436 sheet: -1.20 (0.28), residues: 324 loop : -1.46 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 243 HIS 0.005 0.001 HIS A 220 PHE 0.024 0.002 PHE E 200 TYR 0.033 0.001 TYR R 148 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: A 323 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: A 333 ARG cc_start: 0.6903 (mtm180) cc_final: 0.6602 (ptt180) REVERT: E 180 MET cc_start: 0.6730 (tmm) cc_final: 0.6481 (tmm) REVERT: N 106 ASP cc_start: 0.5190 (t70) cc_final: 0.4947 (t70) REVERT: R 36 VAL cc_start: 0.6105 (p) cc_final: 0.5849 (p) REVERT: R 243 TRP cc_start: 0.6555 (m100) cc_final: 0.6003 (m100) outliers start: 43 outliers final: 16 residues processed: 206 average time/residue: 0.9810 time to fit residues: 219.2095 Evaluate side-chains 163 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 177 ASN Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 247 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11039 Z= 0.332 Angle : 0.719 9.040 14983 Z= 0.370 Chirality : 0.046 0.170 1668 Planarity : 0.006 0.070 1900 Dihedral : 5.890 67.094 1508 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.80 % Allowed : 21.81 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.91 (0.23), residues: 1346 helix: -0.80 (0.24), residues: 436 sheet: -1.20 (0.27), residues: 334 loop : -1.52 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 243 HIS 0.008 0.001 HIS A 220 PHE 0.022 0.002 PHE R 156 TYR 0.034 0.002 TYR R 148 ARG 0.006 0.001 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 147 time to evaluate : 1.287 Fit side-chains REVERT: A 323 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: A 333 ARG cc_start: 0.6986 (mtm180) cc_final: 0.6713 (ptt180) REVERT: B 17 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: B 69 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (mp) REVERT: B 101 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7224 (mmm) REVERT: N 106 ASP cc_start: 0.5500 (t70) cc_final: 0.5228 (t70) REVERT: R 243 TRP cc_start: 0.6691 (m100) cc_final: 0.6169 (m100) REVERT: R 290 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6705 (pt) outliers start: 66 outliers final: 34 residues processed: 190 average time/residue: 0.8630 time to fit residues: 179.0300 Evaluate side-chains 174 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 174 GLN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 234 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11039 Z= 0.194 Angle : 0.630 9.591 14983 Z= 0.322 Chirality : 0.043 0.177 1668 Planarity : 0.005 0.069 1900 Dihedral : 5.447 66.363 1508 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.28 % Allowed : 24.54 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.61 (0.23), residues: 1346 helix: -0.46 (0.25), residues: 437 sheet: -1.10 (0.27), residues: 336 loop : -1.38 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.001 PHE P 6 TYR 0.031 0.001 TYR R 148 ARG 0.008 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 155 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: A 302 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5451 (mt) REVERT: A 323 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 333 ARG cc_start: 0.6934 (mtm180) cc_final: 0.6707 (ptt180) REVERT: B 101 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7119 (mmm) REVERT: E 180 MET cc_start: 0.6794 (tmm) cc_final: 0.6455 (tmm) REVERT: G 63 GLU cc_start: 0.3005 (OUTLIER) cc_final: 0.2381 (tp30) REVERT: N 105 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.4940 (ptm-80) REVERT: P 6 PHE cc_start: 0.7390 (t80) cc_final: 0.7121 (t80) REVERT: R 243 TRP cc_start: 0.6467 (m100) cc_final: 0.5917 (m100) outliers start: 60 outliers final: 23 residues processed: 201 average time/residue: 0.7975 time to fit residues: 174.1345 Evaluate side-chains 161 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN E 174 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11039 Z= 0.198 Angle : 0.645 11.170 14983 Z= 0.325 Chirality : 0.043 0.256 1668 Planarity : 0.005 0.068 1900 Dihedral : 5.264 62.130 1508 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.01 % Allowed : 25.24 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.50 (0.23), residues: 1346 helix: -0.32 (0.25), residues: 437 sheet: -1.03 (0.28), residues: 340 loop : -1.37 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.020 0.001 PHE P 6 TYR 0.030 0.001 TYR R 148 ARG 0.005 0.000 ARG R 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 293 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7708 (mttm) REVERT: A 302 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5370 (mt) REVERT: A 323 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 101 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7107 (mmm) REVERT: B 214 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6574 (ptp-170) REVERT: E 87 ARG cc_start: 0.7227 (mtt90) cc_final: 0.6999 (mtt90) REVERT: E 180 MET cc_start: 0.6760 (tmm) cc_final: 0.6444 (tmm) REVERT: E 211 ASP cc_start: 0.7072 (t0) cc_final: 0.6780 (t0) REVERT: E 232 LYS cc_start: 0.7731 (tptp) cc_final: 0.7522 (tptm) REVERT: G 63 GLU cc_start: 0.3097 (OUTLIER) cc_final: 0.2543 (tp30) REVERT: N 105 ARG cc_start: 0.5393 (OUTLIER) cc_final: 0.4934 (ptm-80) REVERT: R 204 MET cc_start: 0.6077 (ttt) cc_final: 0.5638 (OUTLIER) REVERT: R 226 CYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5666 (m) REVERT: R 243 TRP cc_start: 0.6385 (m100) cc_final: 0.5815 (m100) outliers start: 57 outliers final: 24 residues processed: 188 average time/residue: 0.7282 time to fit residues: 148.6558 Evaluate side-chains 168 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.0010 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN R 234 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11039 Z= 0.176 Angle : 0.630 10.449 14983 Z= 0.316 Chirality : 0.042 0.226 1668 Planarity : 0.005 0.067 1900 Dihedral : 5.111 61.519 1508 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.84 % Allowed : 27.26 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.27 (0.23), residues: 1346 helix: -0.05 (0.26), residues: 436 sheet: -0.89 (0.28), residues: 333 loop : -1.31 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.001 PHE P 22 TYR 0.028 0.001 TYR R 148 ARG 0.012 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: A 35 GLN cc_start: 0.6958 (mp10) cc_final: 0.6724 (mm-40) REVERT: A 208 PHE cc_start: 0.4349 (m-10) cc_final: 0.4031 (m-80) REVERT: A 323 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: B 61 MET cc_start: 0.6863 (pp-130) cc_final: 0.6636 (ppp) REVERT: B 214 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6547 (ptp-170) REVERT: E 87 ARG cc_start: 0.7231 (mtt90) cc_final: 0.6990 (mtt90) REVERT: G 63 GLU cc_start: 0.3102 (OUTLIER) cc_final: 0.2649 (tp30) REVERT: P 26 LEU cc_start: 0.6105 (tm) cc_final: 0.5732 (tp) REVERT: R 40 ARG cc_start: 0.5796 (mpt-90) cc_final: 0.4884 (tpp80) REVERT: R 220 TYR cc_start: 0.5760 (t80) cc_final: 0.5386 (t80) REVERT: R 226 CYS cc_start: 0.6703 (OUTLIER) cc_final: 0.5751 (m) REVERT: R 228 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6380 (tm) REVERT: R 243 TRP cc_start: 0.6421 (m100) cc_final: 0.5859 (m100) REVERT: R 308 ILE cc_start: 0.7400 (tt) cc_final: 0.7080 (mp) outliers start: 55 outliers final: 20 residues processed: 202 average time/residue: 1.0159 time to fit residues: 223.0222 Evaluate side-chains 169 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 234 GLN Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN E 113 GLN E 174 GLN N 39 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11039 Z= 0.227 Angle : 0.685 11.014 14983 Z= 0.344 Chirality : 0.044 0.228 1668 Planarity : 0.005 0.066 1900 Dihedral : 5.153 57.554 1508 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.05 % Allowed : 29.11 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1346 helix: -0.14 (0.25), residues: 436 sheet: -0.97 (0.27), residues: 349 loop : -1.32 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.018 0.001 PHE N 108 TYR 0.030 0.001 TYR R 148 ARG 0.012 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 140 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: A 208 PHE cc_start: 0.4392 (m-10) cc_final: 0.4065 (m-80) REVERT: A 323 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: B 61 MET cc_start: 0.6897 (pp-130) cc_final: 0.6679 (ppp) REVERT: B 214 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6549 (ptp-170) REVERT: E 87 ARG cc_start: 0.7222 (mtt90) cc_final: 0.7012 (mtt90) REVERT: E 208 GLU cc_start: 0.6669 (pm20) cc_final: 0.6278 (pp20) REVERT: G 63 GLU cc_start: 0.3211 (OUTLIER) cc_final: 0.2783 (tp30) REVERT: R 40 ARG cc_start: 0.5850 (mpt-90) cc_final: 0.5322 (ptm160) REVERT: R 142 LEU cc_start: 0.6709 (tm) cc_final: 0.6126 (pp) REVERT: R 220 TYR cc_start: 0.5793 (t80) cc_final: 0.5407 (t80) REVERT: R 226 CYS cc_start: 0.6618 (OUTLIER) cc_final: 0.5746 (m) REVERT: R 243 TRP cc_start: 0.6543 (m100) cc_final: 0.5869 (m100) REVERT: R 308 ILE cc_start: 0.7446 (tt) cc_final: 0.7116 (mp) outliers start: 46 outliers final: 25 residues processed: 172 average time/residue: 1.0853 time to fit residues: 203.0163 Evaluate side-chains 163 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN R 234 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11039 Z= 0.224 Angle : 0.678 10.971 14983 Z= 0.338 Chirality : 0.043 0.221 1668 Planarity : 0.005 0.066 1900 Dihedral : 5.124 53.383 1508 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.13 % Allowed : 29.55 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.28 (0.23), residues: 1346 helix: -0.07 (0.26), residues: 436 sheet: -0.90 (0.28), residues: 340 loop : -1.32 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.030 0.001 PHE P 22 TYR 0.033 0.002 TYR R 148 ARG 0.014 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: A 35 GLN cc_start: 0.6963 (mp10) cc_final: 0.6729 (mm-40) REVERT: A 208 PHE cc_start: 0.4434 (m-10) cc_final: 0.4104 (m-80) REVERT: A 323 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: B 214 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6598 (ptp-170) REVERT: E 87 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6975 (mtt90) REVERT: E 206 ARG cc_start: 0.7924 (tmm160) cc_final: 0.7386 (tmm-80) REVERT: G 63 GLU cc_start: 0.3091 (OUTLIER) cc_final: 0.2686 (tp30) REVERT: P 14 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7283 (mp) REVERT: R 40 ARG cc_start: 0.5775 (mpt-90) cc_final: 0.5078 (tpt-90) REVERT: R 142 LEU cc_start: 0.6710 (tm) cc_final: 0.6129 (pp) REVERT: R 156 PHE cc_start: 0.7317 (t80) cc_final: 0.6930 (t80) REVERT: R 220 TYR cc_start: 0.5805 (t80) cc_final: 0.5490 (t80) REVERT: R 226 CYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5706 (m) REVERT: R 228 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6370 (tm) REVERT: R 308 ILE cc_start: 0.7441 (tt) cc_final: 0.7138 (mt) outliers start: 47 outliers final: 25 residues processed: 174 average time/residue: 1.1177 time to fit residues: 211.1169 Evaluate side-chains 170 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN E 174 GLN R 234 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11039 Z= 0.223 Angle : 0.689 11.487 14983 Z= 0.344 Chirality : 0.043 0.216 1668 Planarity : 0.005 0.070 1900 Dihedral : 5.101 51.429 1508 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.17 % Allowed : 30.61 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.28 (0.23), residues: 1346 helix: -0.05 (0.26), residues: 435 sheet: -0.83 (0.27), residues: 352 loop : -1.37 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.019 0.001 PHE N 108 TYR 0.034 0.001 TYR R 148 ARG 0.014 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: A 208 PHE cc_start: 0.4512 (m-10) cc_final: 0.4214 (m-80) REVERT: A 323 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: B 214 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6535 (ptp-170) REVERT: E 87 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6977 (mtt90) REVERT: G 63 GLU cc_start: 0.3217 (OUTLIER) cc_final: 0.2759 (tp30) REVERT: R 40 ARG cc_start: 0.5814 (mpt-90) cc_final: 0.5100 (tpt-90) REVERT: R 156 PHE cc_start: 0.7313 (t80) cc_final: 0.6923 (t80) REVERT: R 204 MET cc_start: 0.5981 (ttt) cc_final: 0.5540 (ttp) REVERT: R 220 TYR cc_start: 0.5804 (t80) cc_final: 0.5499 (t80) REVERT: R 226 CYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5615 (m) REVERT: R 228 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6338 (tm) REVERT: R 308 ILE cc_start: 0.7402 (tt) cc_final: 0.7117 (mt) outliers start: 36 outliers final: 25 residues processed: 170 average time/residue: 1.1562 time to fit residues: 213.4354 Evaluate side-chains 166 residues out of total 1193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 234 GLN Chi-restraints excluded: chain R residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** R 394 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 = 0.4299 r_free = 0.4299 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129065 restraints weight = 20128.989| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.29 r_work: 0.3797 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 11039 Z= 0.318 Angle : 0.945 59.185 14983 Z= 0.523 Chirality : 0.043 0.201 1668 Planarity : 0.005 0.067 1900 Dihedral : 5.099 51.431 1508 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.69 % Allowed : 30.08 % Favored : 66.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.22 % 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: -1.28 (0.23), residues: 1346 helix: -0.08 (0.26), residues: 435 sheet: -0.89 (0.27), residues: 346 loop : -1.32 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.002 PHE N 29 TYR 0.035 0.001 TYR R 148 ARG 0.012 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.61 seconds wall clock time: 98 minutes 45.99 seconds (5925.99 seconds total)