Starting phenix.real_space_refine on Sun Apr 7 03:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pr4_17834/04_2024/8pr4_17834_updated.pdb" } resolution = 3.5 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= 0.000 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 3 5.49 5 S 57 5.16 5 C 6006 2.51 5 N 1680 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W GLU 12": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9494 Number of models: 1 Model: "" Number of chains: 8 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1262 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1314 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "Y" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2793 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 26, 'TRANS': 348} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "X" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 704 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 200 Chain: "x" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 455 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 190 Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5742 SG CYS Y 30 46.962 79.433 50.441 1.00119.87 S ATOM 5771 SG CYS Y 33 43.721 80.939 49.654 1.00124.84 S ATOM 7246 SG CYS Y 284 44.584 77.361 48.253 1.00116.63 S ATOM 7272 SG CYS Y 287 45.916 80.687 46.863 1.00123.33 S ATOM 5910 SG CYS Y 51 61.662 49.335 53.098 1.00110.92 S ATOM 5929 SG CYS Y 54 65.386 48.865 52.682 1.00119.02 S ATOM 6054 SG CYS Y 70 62.803 47.547 49.966 1.00105.43 S ATOM 6073 SG CYS Y 73 63.592 46.023 53.433 1.00101.62 S ATOM 6095 SG CYS Y 76 55.015 37.387 59.347 1.00 97.69 S ATOM 6112 SG CYS Y 79 54.120 38.479 62.481 1.00106.11 S ATOM 6229 SG CYS Y 111 57.893 37.578 61.880 1.00 98.28 S ATOM 6250 SG CYS Y 114 55.392 34.862 62.376 1.00 94.54 S Time building chain proxies: 5.17, per 1000 atoms: 0.54 Number of scatterers: 9494 At special positions: 0 Unit cell: (109.077, 106.959, 110.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 57 16.00 P 3 15.00 O 1745 8.00 N 1680 7.00 C 6006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.42 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 30 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 284 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 73 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 54 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 79 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 111 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " Number of angles added : 18 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2482 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 16 sheets defined 29.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'J' and resid 61 through 78 Processing helix chain 'J' and resid 99 through 111 Processing helix chain 'J' and resid 125 through 130 removed outlier: 5.017A pdb=" N THR J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 168 through 181 Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 220 through 231 removed outlier: 3.598A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 265 No H-bonds generated for 'chain 'J' and resid 262 through 265' Processing helix chain 'J' and resid 267 through 269 No H-bonds generated for 'chain 'J' and resid 267 through 269' Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.220A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 300 Processing helix chain 'J' and resid 315 through 328 removed outlier: 4.736A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 333 No H-bonds generated for 'chain 'J' and resid 330 through 333' Processing helix chain 'J' and resid 353 through 363 removed outlier: 3.655A pdb=" N ALA J 363 " --> pdb=" O ALA J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 368 No H-bonds generated for 'chain 'J' and resid 365 through 368' Processing helix chain 'J' and resid 375 through 380 Processing helix chain 'U' and resid 66 through 69 No H-bonds generated for 'chain 'U' and resid 66 through 69' Processing helix chain 'U' and resid 162 through 167 Processing helix chain 'W' and resid 165 through 174 Processing helix chain 'Y' and resid 24 through 26 No H-bonds generated for 'chain 'Y' and resid 24 through 26' Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 139 through 169 removed outlier: 4.373A pdb=" N GLN Y 142 " --> pdb=" O PRO Y 139 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG Y 143 " --> pdb=" O HIS Y 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Y 147 " --> pdb=" O MET Y 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU Y 149 " --> pdb=" O LYS Y 146 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN Y 152 " --> pdb=" O GLU Y 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Y 154 " --> pdb=" O TYR Y 151 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL Y 160 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Y 161 " --> pdb=" O GLU Y 158 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG Y 162 " --> pdb=" O LYS Y 159 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP Y 163 " --> pdb=" O VAL Y 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU Y 167 " --> pdb=" O ARG Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 255 No H-bonds generated for 'chain 'Y' and resid 252 through 255' Processing helix chain 'Y' and resid 266 through 268 No H-bonds generated for 'chain 'Y' and resid 266 through 268' Processing helix chain 'Y' and resid 309 through 311 No H-bonds generated for 'chain 'Y' and resid 309 through 311' Processing helix chain 'Y' and resid 449 through 451 No H-bonds generated for 'chain 'Y' and resid 449 through 451' Processing helix chain 'X' and resid 383 through 386 No H-bonds generated for 'chain 'X' and resid 383 through 386' Processing helix chain 'X' and resid 392 through 395 No H-bonds generated for 'chain 'X' and resid 392 through 395' Processing helix chain 'X' and resid 413 through 466 removed outlier: 3.807A pdb=" N VAL X 420 " --> pdb=" O MET X 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU X 423 " --> pdb=" O GLU X 419 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU X 425 " --> pdb=" O GLY X 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU X 430 " --> pdb=" O GLU X 426 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 439 " --> pdb=" O ASN X 435 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL X 440 " --> pdb=" O ALA X 436 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA X 446 " --> pdb=" O ASN X 442 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS X 447 " --> pdb=" O ASP X 443 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP X 449 " --> pdb=" O ILE X 445 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN X 450 " --> pdb=" O ALA X 446 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU X 451 " --> pdb=" O LYS X 447 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL X 457 " --> pdb=" O GLY X 453 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 548 Processing helix chain 'x' and resid 411 through 466 removed outlier: 3.839A pdb=" N VAL x 440 " --> pdb=" O ALA x 436 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU x 462 " --> pdb=" O LEU x 458 " (cutoff:3.500A) Processing helix chain 'x' and resid 519 through 550 removed outlier: 3.588A pdb=" N TYR x 538 " --> pdb=" O GLU x 534 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG x 541 " --> pdb=" O GLN x 537 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET x 543 " --> pdb=" O LYS x 539 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU x 544 " --> pdb=" O GLU x 540 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'J' and resid 118 through 122 removed outlier: 7.083A pdb=" N VAL J 89 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA J 121 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL J 91 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 135 through 141 removed outlier: 3.600A pdb=" N LEU J 164 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY J 162 " --> pdb=" O VAL J 148 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 150 through 152 Processing sheet with id= D, first strand: chain 'J' and resid 246 through 250 Processing sheet with id= E, first strand: chain 'U' and resid 9 through 11 removed outlier: 6.674A pdb=" N VAL U 27 " --> pdb=" O LYS U 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE U 48 " --> pdb=" O THR U 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET U 82 " --> pdb=" O VAL U 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'U' and resid 117 through 119 removed outlier: 6.667A pdb=" N GLU U 135 " --> pdb=" O ILE U 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'W' and resid 6 through 8 removed outlier: 3.510A pdb=" N LEU W 177 " --> pdb=" O LEU W 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR W 8 " --> pdb=" O LEU W 177 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'W' and resid 13 through 15 Processing sheet with id= I, first strand: chain 'W' and resid 144 through 147 removed outlier: 5.837A pdb=" N SER W 147 " --> pdb=" O PHE W 153 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE W 153 " --> pdb=" O SER W 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Y' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'Y' and resid 27 through 30 removed outlier: 3.934A pdb=" N GLU Y 35 " --> pdb=" O CYS Y 30 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Y' and resid 48 through 51 removed outlier: 3.942A pdb=" N SER Y 48 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id= N, first strand: chain 'Y' and resid 406 through 413 removed outlier: 3.741A pdb=" N GLN Y 331 " --> pdb=" O SER Y 320 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER Y 320 " --> pdb=" O GLN Y 331 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU Y 333 " --> pdb=" O ILE Y 318 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE Y 318 " --> pdb=" O LEU Y 333 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR Y 335 " --> pdb=" O VAL Y 316 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL Y 316 " --> pdb=" O THR Y 335 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 340 through 343 Processing sheet with id= P, first strand: chain 'Y' and resid 292 through 294 296 hydrogen bonds defined for protein. 810 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: 2.51 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 3205 1.36 - 1.51: 2860 1.51 - 1.67: 3515 1.67 - 1.83: 75 Bond restraints: 9656 Sorted by residual: bond pdb=" CG PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 1.473 1.572 -0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" C PHE Y 392 " pdb=" N PRO Y 393 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.82e+00 bond pdb=" C ALA U 146 " pdb=" O ALA U 146 " ideal model delta sigma weight residual 1.236 1.270 -0.033 1.26e-02 6.30e+03 7.03e+00 bond pdb=" CB ASN J 275 " pdb=" CG ASN J 275 " ideal model delta sigma weight residual 1.516 1.580 -0.064 2.50e-02 1.60e+03 6.59e+00 ... (remaining 9651 not shown) Histogram of bond angle deviations from ideal: 78.30 - 91.37: 2 91.37 - 104.45: 198 104.45 - 117.52: 6996 117.52 - 130.60: 5908 130.60 - 143.67: 50 Bond angle restraints: 13154 Sorted by residual: angle pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " pdb=" CG PRO Y 369 " ideal model delta sigma weight residual 103.20 78.30 24.90 1.50e+00 4.44e-01 2.76e+02 angle pdb=" CA PRO Y 369 " pdb=" N PRO Y 369 " pdb=" CD PRO Y 369 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" CA PRO Y 369 " pdb=" CB PRO Y 369 " pdb=" CG PRO Y 369 " ideal model delta sigma weight residual 104.50 85.53 18.97 1.90e+00 2.77e-01 9.97e+01 angle pdb=" CA LEU J 96 " pdb=" CB LEU J 96 " pdb=" CG LEU J 96 " ideal model delta sigma weight residual 116.30 143.67 -27.37 3.50e+00 8.16e-02 6.12e+01 angle pdb=" CB MET Y 144 " pdb=" CG MET Y 144 " pdb=" SD MET Y 144 " ideal model delta sigma weight residual 112.70 130.37 -17.67 3.00e+00 1.11e-01 3.47e+01 ... (remaining 13149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 5005 16.62 - 33.24: 615 33.24 - 49.85: 208 49.85 - 66.47: 34 66.47 - 83.09: 13 Dihedral angle restraints: 5875 sinusoidal: 2049 harmonic: 3826 Sorted by residual: dihedral pdb=" CA MET J 126 " pdb=" C MET J 126 " pdb=" N ALA J 127 " pdb=" CA ALA J 127 " ideal model delta harmonic sigma weight residual 180.00 146.03 33.97 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA MET J 311 " pdb=" C MET J 311 " pdb=" N LEU J 312 " pdb=" CA LEU J 312 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLN J 298 " pdb=" C GLN J 298 " pdb=" N LEU J 299 " pdb=" CA LEU J 299 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1387 0.106 - 0.211: 168 0.211 - 0.317: 14 0.317 - 0.423: 2 0.423 - 0.528: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL J 82 " pdb=" CA VAL J 82 " pdb=" CG1 VAL J 82 " pdb=" CG2 VAL J 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" CG LEU Y 282 " pdb=" CB LEU Y 282 " pdb=" CD1 LEU Y 282 " pdb=" CD2 LEU Y 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASN J 275 " pdb=" N ASN J 275 " pdb=" C ASN J 275 " pdb=" CB ASN J 275 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1569 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 368 " -0.118 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO Y 369 " 0.279 5.00e-02 4.00e+02 pdb=" CA PRO Y 369 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO Y 369 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 387 " -0.020 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP J 387 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP J 387 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP J 387 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 387 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 387 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 387 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 387 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 387 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU W 15 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" CD GLU W 15 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU W 15 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU W 15 " 0.023 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2843 2.83 - 3.35: 7837 3.35 - 3.86: 16263 3.86 - 4.38: 16721 4.38 - 4.90: 29346 Nonbonded interactions: 73010 Sorted by model distance: nonbonded pdb=" O ARG X 541 " pdb=" N GLU X 544 " model vdw 2.309 2.520 nonbonded pdb=" OG1 THR U 33 " pdb=" O ASN U 54 " model vdw 2.323 2.440 nonbonded pdb=" O TYR J 377 " pdb=" OG1 THR J 381 " model vdw 2.347 2.440 nonbonded pdb=" OG SER W 18 " pdb=" OD1 ASN W 20 " model vdw 2.350 2.440 nonbonded pdb=" O THR X 379 " pdb=" OG1 THR X 379 " model vdw 2.370 2.440 ... (remaining 73005 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 group one per residue 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 20.490 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.680 Find NCS groups from input model: 0.330 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.460 9656 Z= 0.603 Angle : 1.331 27.371 13154 Z= 0.709 Chirality : 0.068 0.528 1572 Planarity : 0.011 0.162 1702 Dihedral : 17.206 83.088 3393 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.36 % Rotamer: Outliers : 1.00 % Allowed : 28.76 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.40 (0.19), residues: 1296 helix: -2.79 (0.18), residues: 402 sheet: -1.59 (0.36), residues: 190 loop : -2.10 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP J 387 HIS 0.007 0.001 HIS W 90 PHE 0.029 0.002 PHE W 83 TYR 0.018 0.002 TYR J 76 ARG 0.023 0.001 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7629 (t80) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 0.1921 time to fit residues: 27.0689 Evaluate side-chains 80 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain Y residue 305 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 HIS J 351 ASN Y 138 HIS Y 253 GLN Y 306 GLN ** X 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 9656 Z= 0.436 Angle : 0.700 11.713 13154 Z= 0.353 Chirality : 0.046 0.160 1572 Planarity : 0.006 0.068 1702 Dihedral : 6.672 69.664 1435 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.69 % Allowed : 24.08 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1296 helix: 0.03 (0.25), residues: 402 sheet: -1.40 (0.37), residues: 196 loop : -1.73 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 387 HIS 0.004 0.001 HIS U 36 PHE 0.013 0.002 PHE Y 74 TYR 0.014 0.002 TYR Y 312 ARG 0.005 0.001 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 70 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7794 (t80) REVERT: J 137 MET cc_start: 0.8291 (tpp) cc_final: 0.8051 (tpp) REVERT: J 365 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: U 125 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8691 (mp) REVERT: W 176 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8789 (t80) REVERT: Y 253 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8654 (tp-100) REVERT: Y 261 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8331 (p90) REVERT: Y 268 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8382 (mm-40) outliers start: 60 outliers final: 31 residues processed: 123 average time/residue: 0.1775 time to fit residues: 33.1770 Evaluate side-chains 103 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 148 CYS Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 221 ILE Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 253 GLN Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 396 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 162 GLN ** X 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9656 Z= 0.273 Angle : 0.590 10.997 13154 Z= 0.292 Chirality : 0.044 0.138 1572 Planarity : 0.005 0.042 1702 Dihedral : 6.033 77.950 1433 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.35 % Allowed : 24.97 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1296 helix: 1.16 (0.27), residues: 401 sheet: -1.44 (0.35), residues: 223 loop : -1.61 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 387 HIS 0.002 0.001 HIS Y 275 PHE 0.009 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.003 0.000 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 68 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7880 (t80) REVERT: J 137 MET cc_start: 0.8159 (tpp) cc_final: 0.7933 (tpp) REVERT: J 365 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: U 125 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (mp) REVERT: Y 261 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8358 (p90) REVERT: Y 319 MET cc_start: 0.8452 (pmm) cc_final: 0.8104 (pmm) outliers start: 48 outliers final: 32 residues processed: 107 average time/residue: 0.1837 time to fit residues: 29.6337 Evaluate side-chains 103 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 67 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 396 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 78 optimal weight: 0.0170 chunk 116 optimal weight: 0.0570 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9656 Z= 0.213 Angle : 0.544 10.136 13154 Z= 0.268 Chirality : 0.043 0.141 1572 Planarity : 0.004 0.038 1702 Dihedral : 5.555 81.126 1433 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.57 % Allowed : 24.41 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1296 helix: 1.70 (0.27), residues: 402 sheet: -1.45 (0.36), residues: 213 loop : -1.46 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 387 HIS 0.002 0.000 HIS J 79 PHE 0.008 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.003 0.000 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 71 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8006 (t80) REVERT: J 126 MET cc_start: 0.9091 (mtm) cc_final: 0.8516 (mtt) REVERT: J 137 MET cc_start: 0.7922 (tpp) cc_final: 0.7482 (tpt) REVERT: J 286 ASP cc_start: 0.8756 (m-30) cc_final: 0.8194 (m-30) REVERT: J 365 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: J 380 GLN cc_start: 0.8635 (pp30) cc_final: 0.7991 (pp30) REVERT: U 125 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8631 (mp) REVERT: W 176 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8798 (t80) REVERT: Y 261 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8284 (p90) REVERT: Y 268 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8339 (mm-40) REVERT: Y 319 MET cc_start: 0.8359 (pmm) cc_final: 0.8123 (pmm) outliers start: 50 outliers final: 33 residues processed: 114 average time/residue: 0.1916 time to fit residues: 32.9639 Evaluate side-chains 109 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 70 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 ASN W 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9656 Z= 0.419 Angle : 0.648 11.048 13154 Z= 0.322 Chirality : 0.046 0.178 1572 Planarity : 0.004 0.039 1702 Dihedral : 5.832 76.176 1433 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 7.13 % Allowed : 23.97 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1296 helix: 1.79 (0.27), residues: 404 sheet: -1.57 (0.35), residues: 200 loop : -1.43 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 355 HIS 0.003 0.001 HIS Y 81 PHE 0.011 0.001 PHE Y 74 TYR 0.008 0.001 TYR Y 240 ARG 0.004 0.001 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 68 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7988 (t80) REVERT: J 126 MET cc_start: 0.9053 (mtm) cc_final: 0.8324 (mtt) REVERT: J 286 ASP cc_start: 0.8701 (m-30) cc_final: 0.8203 (m-30) REVERT: J 365 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: J 387 TRP cc_start: 0.8455 (p-90) cc_final: 0.6666 (m100) REVERT: W 5 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8289 (mm-30) REVERT: W 162 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8287 (tp40) REVERT: W 176 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8755 (t80) REVERT: Y 261 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8282 (p90) REVERT: Y 268 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8436 (mm-40) outliers start: 64 outliers final: 44 residues processed: 125 average time/residue: 0.1814 time to fit residues: 34.1761 Evaluate side-chains 117 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 68 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 26 GLN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN Chi-restraints excluded: chain Y residue 297 ASN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9656 Z= 0.166 Angle : 0.535 10.570 13154 Z= 0.261 Chirality : 0.043 0.139 1572 Planarity : 0.004 0.034 1702 Dihedral : 5.363 83.765 1433 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.13 % Allowed : 25.86 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1296 helix: 2.16 (0.27), residues: 414 sheet: -1.40 (0.36), residues: 211 loop : -1.27 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 355 HIS 0.002 0.000 HIS Y 49 PHE 0.008 0.001 PHE J 113 TYR 0.009 0.001 TYR Y 32 ARG 0.004 0.000 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8074 (t80) REVERT: J 286 ASP cc_start: 0.8688 (m-30) cc_final: 0.8195 (m-30) REVERT: J 365 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7257 (mt0) REVERT: W 162 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8138 (tp40) REVERT: W 176 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8670 (t80) REVERT: Y 26 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: Y 261 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8261 (p90) REVERT: Y 268 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: Y 319 MET cc_start: 0.8393 (pmm) cc_final: 0.8016 (pmm) outliers start: 46 outliers final: 29 residues processed: 113 average time/residue: 0.1836 time to fit residues: 31.1580 Evaluate side-chains 104 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 69 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 26 GLN Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 268 GLN Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 0.0870 chunk 104 optimal weight: 0.0970 chunk 69 optimal weight: 0.0040 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN U 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9656 Z= 0.141 Angle : 0.524 10.212 13154 Z= 0.255 Chirality : 0.042 0.162 1572 Planarity : 0.003 0.033 1702 Dihedral : 5.018 81.134 1433 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.79 % Allowed : 27.20 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1296 helix: 2.53 (0.27), residues: 407 sheet: -1.32 (0.37), residues: 200 loop : -1.08 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 355 HIS 0.002 0.000 HIS Y 49 PHE 0.008 0.001 PHE J 113 TYR 0.008 0.001 TYR Y 32 ARG 0.004 0.000 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7987 (t80) REVERT: J 140 ASP cc_start: 0.8180 (t0) cc_final: 0.7834 (t0) REVERT: J 286 ASP cc_start: 0.8724 (m-30) cc_final: 0.8259 (m-30) REVERT: J 365 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: U 131 LEU cc_start: 0.8948 (pp) cc_final: 0.8719 (pp) REVERT: W 1 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5789 (ptm) REVERT: W 162 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7986 (tp40) REVERT: W 176 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8654 (t80) REVERT: Y 261 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8346 (p90) outliers start: 34 outliers final: 26 residues processed: 106 average time/residue: 0.1825 time to fit residues: 29.4078 Evaluate side-chains 102 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 71 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN U 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9656 Z= 0.168 Angle : 0.530 10.860 13154 Z= 0.256 Chirality : 0.043 0.141 1572 Planarity : 0.003 0.032 1702 Dihedral : 4.957 78.693 1433 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.57 % Allowed : 26.20 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1296 helix: 2.58 (0.27), residues: 413 sheet: -1.26 (0.37), residues: 200 loop : -1.00 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 355 HIS 0.002 0.000 HIS Y 49 PHE 0.007 0.001 PHE J 113 TYR 0.009 0.001 TYR Y 12 ARG 0.004 0.000 ARG U 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 74 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7936 (t80) REVERT: J 140 ASP cc_start: 0.8172 (t0) cc_final: 0.7819 (t0) REVERT: J 286 ASP cc_start: 0.8685 (m-30) cc_final: 0.8216 (m-30) REVERT: J 365 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: U 131 LEU cc_start: 0.8969 (pp) cc_final: 0.8758 (pp) REVERT: W 1 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5620 (ptm) REVERT: W 162 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7994 (tp40) REVERT: W 176 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8660 (t80) REVERT: Y 5 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8157 (pp) REVERT: Y 261 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8382 (p90) outliers start: 41 outliers final: 28 residues processed: 111 average time/residue: 0.1871 time to fit residues: 30.7357 Evaluate side-chains 105 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 71 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 275 ASN ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9656 Z= 0.393 Angle : 0.643 12.657 13154 Z= 0.318 Chirality : 0.045 0.142 1572 Planarity : 0.004 0.038 1702 Dihedral : 5.470 75.574 1433 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.35 % Allowed : 25.75 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1296 helix: 2.38 (0.27), residues: 413 sheet: -1.45 (0.34), residues: 240 loop : -1.23 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Y 133 HIS 0.003 0.001 HIS J 79 PHE 0.011 0.001 PHE Y 74 TYR 0.008 0.001 TYR Y 312 ARG 0.003 0.000 ARG J 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 68 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8074 (t80) REVERT: J 286 ASP cc_start: 0.8654 (m-30) cc_final: 0.8197 (m-30) REVERT: J 365 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: J 387 TRP cc_start: 0.8500 (p-90) cc_final: 0.6595 (m100) REVERT: W 176 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8665 (t80) REVERT: Y 5 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (pp) REVERT: Y 261 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8310 (p90) outliers start: 48 outliers final: 38 residues processed: 108 average time/residue: 0.1851 time to fit residues: 30.3111 Evaluate side-chains 110 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 67 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 275 ASN Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 107 ILE Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain U residue 153 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9656 Z= 0.196 Angle : 0.556 11.627 13154 Z= 0.273 Chirality : 0.043 0.144 1572 Planarity : 0.004 0.033 1702 Dihedral : 5.219 79.852 1433 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.24 % Allowed : 26.98 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1296 helix: 2.53 (0.27), residues: 413 sheet: -1.49 (0.35), residues: 211 loop : -1.04 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 355 HIS 0.004 0.001 HIS J 124 PHE 0.007 0.001 PHE U 134 TYR 0.008 0.001 TYR Y 32 ARG 0.004 0.000 ARG J 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 71 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 76 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8058 (t80) REVERT: J 286 ASP cc_start: 0.8628 (m-30) cc_final: 0.8182 (m-30) REVERT: J 365 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: J 387 TRP cc_start: 0.8459 (p-90) cc_final: 0.6537 (m100) REVERT: W 1 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5919 (ptm) REVERT: W 176 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (t80) REVERT: Y 5 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8297 (pp) REVERT: Y 261 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8394 (p90) outliers start: 38 outliers final: 28 residues processed: 103 average time/residue: 0.1941 time to fit residues: 29.7986 Evaluate side-chains 101 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 67 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 231 PHE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 131 LEU Chi-restraints excluded: chain U residue 132 ASN Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 152 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 LEU Chi-restraints excluded: chain W residue 20 ASN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 54 ASN Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 118 SER Chi-restraints excluded: chain Y residue 232 VAL Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 244 VAL Chi-restraints excluded: chain Y residue 261 PHE Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 305 ILE Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054650 restraints weight = 32176.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056407 restraints weight = 17200.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057581 restraints weight = 11711.981| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9656 Z= 0.202 Angle : 0.555 11.415 13154 Z= 0.271 Chirality : 0.043 0.139 1572 Planarity : 0.004 0.033 1702 Dihedral : 5.146 78.736 1433 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.24 % Allowed : 26.98 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1296 helix: 2.54 (0.27), residues: 413 sheet: -1.49 (0.36), residues: 201 loop : -1.04 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 355 HIS 0.004 0.000 HIS J 124 PHE 0.015 0.001 PHE W 83 TYR 0.007 0.001 TYR Y 32 ARG 0.004 0.000 ARG J 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.09 seconds wall clock time: 40 minutes 13.53 seconds (2413.53 seconds total)