Starting phenix.real_space_refine on Fri Mar 15 16:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yot_33986/03_2024/7yot_33986.pdb" } resolution = 3.0 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= 0.008 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 76 5.16 5 C 7714 2.51 5 N 2126 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 300": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1077": "NH1" <-> "NH2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A ARG 1093": "NH1" <-> "NH2" Residue "A ARG 1101": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ARG 1189": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12182 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 51, 371 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Conformer: "B" Number of residues, atoms: 51, 371 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} bond proxies already assigned to first conformer: 367 Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 303 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "B" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 244 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 849 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 11, 'TRANS': 103} Chain breaks: 2 Chain: "A" Number of atoms: 10410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10410 Classifications: {'peptide': 1309} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1251} Chain breaks: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA D 301 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 301 " occ=0.50 Time building chain proxies: 6.89, per 1000 atoms: 0.57 Number of scatterers: 12182 At special positions: 0 Unit cell: (102.96, 112.32, 111.28, 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 76 16.00 O 2266 8.00 N 2126 7.00 C 7714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1350 " distance=2.03 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1160 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.5 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2962 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 7 sheets defined 54.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'D' and resid 262 through 281 removed outlier: 3.535A pdb=" N ALA D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.667A pdb=" N ARG D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.713A pdb=" N THR C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.842A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.898A pdb=" N ALA E 278 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 279 " --> pdb=" O MET E 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 279' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 352 through 366 removed outlier: 3.586A pdb=" N VAL E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.514A pdb=" N GLN A 12 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 13 " --> pdb=" O GLU A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 9 through 13' Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.934A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.067A pdb=" N ASP A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 63 through 80 removed outlier: 4.001A pdb=" N MET A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.540A pdb=" N GLY A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 141 removed outlier: 3.509A pdb=" N ASN A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.970A pdb=" N THR A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 removed outlier: 3.540A pdb=" N VAL A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.646A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.023A pdb=" N LEU A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.732A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.642A pdb=" N LEU A 356 " --> pdb=" O MET A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.153A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 416 through 420 removed outlier: 4.053A pdb=" N ILE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.753A pdb=" N ALA A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.752A pdb=" N PHE A 484 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.526A pdb=" N LEU A 489 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.533A pdb=" N ASN A 496 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 497 " --> pdb=" O LYS A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 497' Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 558 through 576 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.561A pdb=" N LEU A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 649 removed outlier: 3.951A pdb=" N TRP A 649 " --> pdb=" O CYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 5.485A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.908A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 721 through 739 removed outlier: 3.568A pdb=" N TRP A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 Processing helix chain 'A' and resid 823 through 829 removed outlier: 3.643A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.681A pdb=" N SER A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 901 through 911 Processing helix chain 'A' and resid 922 through 926 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 952 through 961 removed outlier: 4.394A pdb=" N MET A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 986 through 1000 removed outlier: 3.580A pdb=" N PHE A1000 " --> pdb=" O GLN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1045 through 1055 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1075 through 1083 Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1112 through 1125 Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.513A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1230 removed outlier: 3.585A pdb=" N TYR A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1244 Processing helix chain 'A' and resid 1251 through 1256 removed outlier: 3.809A pdb=" N ARG A1255 " --> pdb=" O SER A1251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1251 through 1256' Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.647A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1327 removed outlier: 3.506A pdb=" N LEU A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.493A pdb=" N LYS B 284 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.623A pdb=" N GLY A 207 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556 removed outlier: 4.825A pdb=" N VAL A 538 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 684 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 748 removed outlier: 4.338A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN A 795 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 748 removed outlier: 4.338A pdb=" N ARG A 743 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 810 Processing sheet with id=AA7, first strand: chain 'A' and resid 1292 through 1294 removed outlier: 3.541A pdb=" N THR A1168 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A1339 " --> pdb=" O LEU A1172 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1621 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: 4.26 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3015 1.33 - 1.45: 2500 1.45 - 1.58: 6782 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 12420 Sorted by residual: bond pdb=" CG1 ILE A 117 " pdb=" CD1 ILE A 117 " ideal model delta sigma weight residual 1.513 1.394 0.119 3.90e-02 6.57e+02 9.32e+00 bond pdb=" CG LEU A 647 " pdb=" CD1 LEU A 647 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.18e+00 bond pdb=" CB VAL A 748 " pdb=" CG1 VAL A 748 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.62e+00 bond pdb=" CG1 ILE A 267 " pdb=" CD1 ILE A 267 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.41e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.506 1.419 0.087 3.90e-02 6.57e+02 4.97e+00 ... (remaining 12415 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.51: 184 103.51 - 111.15: 4748 111.15 - 118.79: 5256 118.79 - 126.43: 6433 126.43 - 134.07: 197 Bond angle restraints: 16818 Sorted by residual: angle pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" CA LEU A1008 " pdb=" CB LEU A1008 " pdb=" CG LEU A1008 " ideal model delta sigma weight residual 116.30 132.82 -16.52 3.50e+00 8.16e-02 2.23e+01 angle pdb=" CA LEU E 286 " pdb=" CB LEU E 286 " pdb=" CG LEU E 286 " ideal model delta sigma weight residual 116.30 132.35 -16.05 3.50e+00 8.16e-02 2.10e+01 angle pdb=" C ASN A 463 " pdb=" N LEU A 464 " pdb=" CA LEU A 464 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" N ILE A 792 " pdb=" CA ILE A 792 " pdb=" C ILE A 792 " ideal model delta sigma weight residual 112.29 108.60 3.69 9.40e-01 1.13e+00 1.54e+01 ... (remaining 16813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 7151 15.58 - 31.16: 329 31.16 - 46.74: 93 46.74 - 62.32: 6 62.32 - 77.90: 11 Dihedral angle restraints: 7590 sinusoidal: 3048 harmonic: 4542 Sorted by residual: dihedral pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual 93.00 170.90 -77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CA ASN A 705 " pdb=" C ASN A 705 " pdb=" N ASP A 706 " pdb=" CA ASP A 706 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA THR A 526 " pdb=" C THR A 526 " pdb=" N THR A 527 " pdb=" CA THR A 527 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1322 0.056 - 0.112: 503 0.112 - 0.168: 103 0.168 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CB VAL A1037 " pdb=" CA VAL A1037 " pdb=" CG1 VAL A1037 " pdb=" CG2 VAL A1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL E 335 " pdb=" CA VAL E 335 " pdb=" CG1 VAL E 335 " pdb=" CG2 VAL E 335 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 489 " pdb=" CB LEU A 489 " pdb=" CD1 LEU A 489 " pdb=" CD2 LEU A 489 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1936 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " -0.021 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP A 33 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.021 2.00e-02 2.50e+03 2.87e-02 1.45e+01 pdb=" CG PHE A 395 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 265 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ASP A 265 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP A 265 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 266 " -0.018 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3199 2.80 - 3.33: 10898 3.33 - 3.85: 20215 3.85 - 4.38: 24316 4.38 - 4.90: 41786 Nonbonded interactions: 100414 Sorted by model distance: nonbonded pdb=" OG SER A1108 " pdb=" OD1 ASP A1110 " model vdw 2.279 2.440 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASP A 245 " model vdw 2.281 2.440 nonbonded pdb=" NH1 ARG A 319 " pdb=" OD1 ASP A 332 " model vdw 2.324 2.520 nonbonded pdb=" OG SER E 385 " pdb=" O GLU E 387 " model vdw 2.337 2.440 nonbonded pdb=" O LEU A1145 " pdb=" OG SER A1348 " model vdw 2.342 2.440 ... (remaining 100409 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.350 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.220 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.170 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: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.009 0.119 12420 Z= 0.565 Angle : 1.030 16.518 16818 Z= 0.530 Chirality : 0.059 0.279 1939 Planarity : 0.008 0.065 2144 Dihedral : 10.474 76.529 4622 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.66 % Allowed : 2.93 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.17), residues: 1526 helix: -2.58 (0.13), residues: 762 sheet: -0.81 (0.57), residues: 85 loop : -2.29 (0.20), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP A 33 HIS 0.013 0.003 HIS A 178 PHE 0.061 0.004 PHE A 395 TYR 0.035 0.003 TYR A 868 ARG 0.013 0.002 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 292 time to evaluate : 1.280 Fit side-chains REVERT: D 304 LYS cc_start: 0.7974 (mttt) cc_final: 0.7302 (mmtt) REVERT: B 287 ASP cc_start: 0.8159 (t70) cc_final: 0.7806 (t70) REVERT: E 325 GLU cc_start: 0.7978 (pt0) cc_final: 0.7560 (pt0) REVERT: E 378 SER cc_start: 0.8341 (m) cc_final: 0.8133 (m) REVERT: A 96 GLU cc_start: 0.7669 (tt0) cc_final: 0.7425 (tt0) REVERT: A 137 LYS cc_start: 0.8114 (tttt) cc_final: 0.7753 (ttmm) REVERT: A 769 SER cc_start: 0.8767 (m) cc_final: 0.8404 (p) REVERT: A 956 MET cc_start: 0.8831 (tpt) cc_final: 0.8541 (tpp) REVERT: A 989 ILE cc_start: 0.8716 (mt) cc_final: 0.8489 (mp) REVERT: A 997 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7125 (mtm110) REVERT: A 1087 MET cc_start: 0.8719 (mtp) cc_final: 0.8472 (mtm) REVERT: A 1174 SER cc_start: 0.8638 (t) cc_final: 0.8201 (t) REVERT: A 1222 SER cc_start: 0.8583 (m) cc_final: 0.8367 (p) REVERT: A 1340 THR cc_start: 0.7360 (p) cc_final: 0.6961 (m) outliers start: 9 outliers final: 3 residues processed: 299 average time/residue: 1.2879 time to fit residues: 415.8094 Evaluate side-chains 195 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 1037 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0470 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.0060 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 HIS E 369 HIS A 54 GLN A 78 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 336 HIS A 348 ASN A 463 ASN A 487 ASN A 565 GLN A 575 GLN A 652 GLN A 662 ASN A 669 HIS ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS A 922 GLN A 974 ASN A1088 HIS A1235 ASN A1292 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12420 Z= 0.141 Angle : 0.524 9.378 16818 Z= 0.266 Chirality : 0.040 0.155 1939 Planarity : 0.005 0.044 2144 Dihedral : 4.947 47.319 1669 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.64 % Allowed : 10.55 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.41 (0.20), residues: 1526 helix: -0.36 (0.18), residues: 743 sheet: -0.54 (0.57), residues: 85 loop : -1.58 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 33 HIS 0.005 0.001 HIS A 27 PHE 0.017 0.001 PHE A 395 TYR 0.013 0.001 TYR A 524 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.396 Fit side-chains REVERT: D 304 LYS cc_start: 0.7794 (mttt) cc_final: 0.7227 (mmtt) REVERT: B 282 MET cc_start: 0.6855 (mmt) cc_final: 0.6548 (mmt) REVERT: B 287 ASP cc_start: 0.8073 (t70) cc_final: 0.7745 (t70) REVERT: B 300 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8522 (mtm-85) REVERT: E 325 GLU cc_start: 0.7939 (pt0) cc_final: 0.7611 (pt0) REVERT: A 96 GLU cc_start: 0.7657 (tt0) cc_final: 0.7426 (tt0) REVERT: A 137 LYS cc_start: 0.7911 (tttt) cc_final: 0.7660 (ttmm) REVERT: A 520 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8224 (ttpp) REVERT: A 760 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: A 896 GLN cc_start: 0.7167 (mp10) cc_final: 0.6643 (mm-40) REVERT: A 956 MET cc_start: 0.8806 (tpt) cc_final: 0.8567 (tpp) REVERT: A 989 ILE cc_start: 0.8770 (mt) cc_final: 0.8527 (mp) REVERT: A 997 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7153 (mtm110) REVERT: A 1052 GLN cc_start: 0.8306 (tt0) cc_final: 0.8078 (mt0) REVERT: A 1090 MET cc_start: 0.8203 (mmm) cc_final: 0.7981 (tpt) REVERT: A 1211 MET cc_start: 0.6023 (mtm) cc_final: 0.5483 (ptt) REVERT: A 1334 LYS cc_start: 0.7747 (mttt) cc_final: 0.6981 (mptt) REVERT: A 1340 THR cc_start: 0.7403 (p) cc_final: 0.7041 (m) outliers start: 36 outliers final: 16 residues processed: 242 average time/residue: 1.2104 time to fit residues: 319.3724 Evaluate side-chains 190 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 268 GLN A 54 GLN A 78 GLN A 120 HIS A 463 ASN A 478 ASN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1171 HIS A1292 HIS A1314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12420 Z= 0.274 Angle : 0.577 10.788 16818 Z= 0.288 Chirality : 0.043 0.158 1939 Planarity : 0.004 0.043 2144 Dihedral : 4.956 56.783 1669 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.81 % Allowed : 12.89 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.21), residues: 1526 helix: 0.27 (0.19), residues: 751 sheet: -0.17 (0.59), residues: 85 loop : -1.22 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 33 HIS 0.008 0.001 HIS A 178 PHE 0.025 0.002 PHE A 395 TYR 0.016 0.002 TYR A 868 ARG 0.004 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.302 Fit side-chains REVERT: D 304 LYS cc_start: 0.7829 (mttt) cc_final: 0.7343 (mmtt) REVERT: B 282 MET cc_start: 0.6754 (mmt) cc_final: 0.5964 (mmt) REVERT: B 287 ASP cc_start: 0.8090 (t70) cc_final: 0.7835 (t70) REVERT: B 300 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8590 (mtm-85) REVERT: E 325 GLU cc_start: 0.7976 (pt0) cc_final: 0.7655 (pt0) REVERT: A 96 GLU cc_start: 0.7670 (tt0) cc_final: 0.7427 (tt0) REVERT: A 137 LYS cc_start: 0.7820 (tttt) cc_final: 0.7545 (ttmm) REVERT: A 520 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8222 (ttpp) REVERT: A 896 GLN cc_start: 0.7155 (mp10) cc_final: 0.6636 (mm-40) REVERT: A 956 MET cc_start: 0.8852 (tpt) cc_final: 0.8607 (tpp) REVERT: A 989 ILE cc_start: 0.8732 (mt) cc_final: 0.8510 (mp) REVERT: A 997 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7165 (mtm110) REVERT: A 1090 MET cc_start: 0.8281 (mmm) cc_final: 0.8034 (tpt) REVERT: A 1111 MET cc_start: 0.8117 (mtp) cc_final: 0.7883 (mtt) REVERT: A 1133 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.7978 (mmtp) REVERT: A 1340 THR cc_start: 0.7403 (p) cc_final: 0.7017 (m) outliers start: 52 outliers final: 30 residues processed: 217 average time/residue: 1.2212 time to fit residues: 288.3703 Evaluate side-chains 200 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 78 GLN A 463 ASN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12420 Z= 0.305 Angle : 0.577 10.388 16818 Z= 0.289 Chirality : 0.044 0.176 1939 Planarity : 0.004 0.043 2144 Dihedral : 4.761 47.455 1668 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.32 % Allowed : 13.48 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.36 (0.22), residues: 1526 helix: 0.46 (0.19), residues: 752 sheet: 0.37 (0.62), residues: 72 loop : -1.04 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 33 HIS 0.008 0.001 HIS A 178 PHE 0.021 0.002 PHE A 395 TYR 0.014 0.002 TYR A 977 ARG 0.003 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 176 time to evaluate : 1.331 Fit side-chains REVERT: D 304 LYS cc_start: 0.7844 (mttt) cc_final: 0.7297 (mmtt) REVERT: B 282 MET cc_start: 0.6757 (mmt) cc_final: 0.5891 (mmt) REVERT: B 300 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8673 (mtm-85) REVERT: E 325 GLU cc_start: 0.8011 (pt0) cc_final: 0.7605 (pt0) REVERT: A 96 GLU cc_start: 0.7707 (tt0) cc_final: 0.7454 (tt0) REVERT: A 137 LYS cc_start: 0.7858 (tttt) cc_final: 0.7566 (ttmm) REVERT: A 173 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8762 (ttpt) REVERT: A 359 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 520 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8223 (ttpp) REVERT: A 680 ASP cc_start: 0.8459 (t0) cc_final: 0.8203 (t0) REVERT: A 776 GLU cc_start: 0.7576 (tt0) cc_final: 0.7229 (mm-30) REVERT: A 956 MET cc_start: 0.8856 (tpt) cc_final: 0.8546 (tpp) REVERT: A 989 ILE cc_start: 0.8761 (mt) cc_final: 0.8539 (mp) REVERT: A 997 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7146 (mtm110) REVERT: A 1025 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 1090 MET cc_start: 0.8309 (mmm) cc_final: 0.8016 (tpt) REVERT: A 1133 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.7974 (mmtp) REVERT: A 1249 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (pp) REVERT: A 1340 THR cc_start: 0.7398 (p) cc_final: 0.7010 (m) outliers start: 59 outliers final: 32 residues processed: 216 average time/residue: 1.2036 time to fit residues: 283.2621 Evaluate side-chains 208 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1337 ASP Chi-restraints excluded: chain A residue 1363 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 HIS A 54 GLN A 78 GLN A 314 ASN A 463 ASN A 475 HIS ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12420 Z= 0.162 Angle : 0.493 10.344 16818 Z= 0.248 Chirality : 0.040 0.158 1939 Planarity : 0.004 0.041 2144 Dihedral : 4.402 43.896 1668 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.22 % Allowed : 14.58 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.02 (0.22), residues: 1526 helix: 0.83 (0.19), residues: 756 sheet: 0.34 (0.62), residues: 72 loop : -0.89 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 PHE 0.014 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.004 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.630 Fit side-chains REVERT: D 283 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: D 304 LYS cc_start: 0.7783 (mttt) cc_final: 0.7396 (mptt) REVERT: B 300 ARG cc_start: 0.8897 (mtt180) cc_final: 0.8670 (mtm-85) REVERT: E 325 GLU cc_start: 0.7970 (pt0) cc_final: 0.7650 (pt0) REVERT: A 96 GLU cc_start: 0.7714 (tt0) cc_final: 0.7454 (tt0) REVERT: A 137 LYS cc_start: 0.7822 (tttt) cc_final: 0.7560 (ttmm) REVERT: A 277 ASP cc_start: 0.8095 (p0) cc_final: 0.7845 (p0) REVERT: A 520 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8181 (ttpp) REVERT: A 680 ASP cc_start: 0.8400 (t0) cc_final: 0.8149 (t0) REVERT: A 776 GLU cc_start: 0.7563 (tt0) cc_final: 0.7219 (mm-30) REVERT: A 896 GLN cc_start: 0.7186 (mp10) cc_final: 0.6657 (mm110) REVERT: A 956 MET cc_start: 0.8835 (tpt) cc_final: 0.8569 (tpp) REVERT: A 989 ILE cc_start: 0.8723 (mt) cc_final: 0.8496 (mp) REVERT: A 997 ARG cc_start: 0.7448 (mtp180) cc_final: 0.7113 (mtm110) REVERT: A 1042 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7608 (ttp) REVERT: A 1090 MET cc_start: 0.8232 (mmm) cc_final: 0.8015 (tpt) REVERT: A 1111 MET cc_start: 0.8102 (mtp) cc_final: 0.7884 (mtt) REVERT: A 1133 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7973 (mmtp) REVERT: A 1331 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8518 (t) REVERT: A 1334 LYS cc_start: 0.7715 (mttt) cc_final: 0.6914 (mptt) REVERT: A 1340 THR cc_start: 0.7307 (p) cc_final: 0.6938 (m) outliers start: 44 outliers final: 22 residues processed: 201 average time/residue: 1.2359 time to fit residues: 271.6064 Evaluate side-chains 197 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 148 optimal weight: 0.0670 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 463 ASN A 475 HIS A 749 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12420 Z= 0.127 Angle : 0.468 9.397 16818 Z= 0.236 Chirality : 0.039 0.154 1939 Planarity : 0.004 0.040 2144 Dihedral : 4.177 41.721 1668 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 15.68 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.35 (0.22), residues: 1526 helix: 1.13 (0.19), residues: 752 sheet: 0.34 (0.60), residues: 76 loop : -0.75 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.009 0.001 HIS A 475 PHE 0.015 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.003 0.000 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.324 Fit side-chains REVERT: D 304 LYS cc_start: 0.7790 (mttt) cc_final: 0.7267 (mmtt) REVERT: C 272 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8721 (m) REVERT: E 325 GLU cc_start: 0.7982 (pt0) cc_final: 0.7660 (pt0) REVERT: A 96 GLU cc_start: 0.7667 (tt0) cc_final: 0.7344 (tt0) REVERT: A 137 LYS cc_start: 0.7797 (tttt) cc_final: 0.7563 (ttmm) REVERT: A 543 LYS cc_start: 0.7614 (ptpt) cc_final: 0.7205 (mttt) REVERT: A 776 GLU cc_start: 0.7560 (tt0) cc_final: 0.7219 (mm-30) REVERT: A 896 GLN cc_start: 0.7168 (mp10) cc_final: 0.6627 (mm110) REVERT: A 956 MET cc_start: 0.8850 (tpt) cc_final: 0.8595 (tpp) REVERT: A 961 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 997 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7134 (mtm110) REVERT: A 1042 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7620 (ttp) REVERT: A 1052 GLN cc_start: 0.8293 (tt0) cc_final: 0.8091 (mt0) REVERT: A 1090 MET cc_start: 0.8214 (mmm) cc_final: 0.7999 (tpt) REVERT: A 1111 MET cc_start: 0.8036 (mtp) cc_final: 0.7815 (mtt) REVERT: A 1133 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7966 (mmtp) REVERT: A 1249 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8391 (pp) REVERT: A 1334 LYS cc_start: 0.7737 (mttt) cc_final: 0.6925 (mptt) REVERT: A 1340 THR cc_start: 0.7219 (p) cc_final: 0.6901 (m) outliers start: 38 outliers final: 21 residues processed: 193 average time/residue: 1.2466 time to fit residues: 261.5779 Evaluate side-chains 194 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 197 ASN A 463 ASN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12420 Z= 0.241 Angle : 0.525 9.610 16818 Z= 0.263 Chirality : 0.042 0.162 1939 Planarity : 0.004 0.047 2144 Dihedral : 4.382 45.658 1668 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.08 % Allowed : 16.19 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.30 (0.22), residues: 1526 helix: 1.04 (0.19), residues: 755 sheet: 0.52 (0.62), residues: 72 loop : -0.73 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.011 0.001 HIS A 475 PHE 0.015 0.001 PHE A 395 TYR 0.012 0.001 TYR A 283 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.579 Fit side-chains REVERT: D 304 LYS cc_start: 0.7832 (mttt) cc_final: 0.7456 (mptt) REVERT: C 272 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8748 (m) REVERT: E 325 GLU cc_start: 0.7981 (pt0) cc_final: 0.7628 (pt0) REVERT: A 96 GLU cc_start: 0.7639 (tt0) cc_final: 0.7398 (tt0) REVERT: A 137 LYS cc_start: 0.7835 (tttt) cc_final: 0.7581 (ttmm) REVERT: A 277 ASP cc_start: 0.8062 (p0) cc_final: 0.7785 (p0) REVERT: A 520 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8198 (ttpp) REVERT: A 776 GLU cc_start: 0.7576 (tt0) cc_final: 0.7233 (mm-30) REVERT: A 826 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8181 (mtpt) REVERT: A 896 GLN cc_start: 0.7211 (mp10) cc_final: 0.6658 (mm110) REVERT: A 956 MET cc_start: 0.8824 (tpt) cc_final: 0.8578 (tpp) REVERT: A 1042 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7734 (ttp) REVERT: A 1090 MET cc_start: 0.8256 (mmm) cc_final: 0.8035 (tpt) REVERT: A 1111 MET cc_start: 0.7986 (mtp) cc_final: 0.7774 (mtt) REVERT: A 1133 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7924 (mmtp) REVERT: A 1249 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8463 (pp) REVERT: A 1331 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8541 (t) REVERT: A 1334 LYS cc_start: 0.7824 (mttt) cc_final: 0.7004 (mptt) REVERT: A 1340 THR cc_start: 0.7335 (p) cc_final: 0.7001 (m) outliers start: 42 outliers final: 23 residues processed: 193 average time/residue: 1.2601 time to fit residues: 265.7938 Evaluate side-chains 192 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1086 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 377 GLN A 463 ASN A 475 HIS A1314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12420 Z= 0.144 Angle : 0.473 9.132 16818 Z= 0.238 Chirality : 0.040 0.145 1939 Planarity : 0.004 0.040 2144 Dihedral : 4.162 42.069 1668 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.49 % Allowed : 16.63 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.52 (0.22), residues: 1526 helix: 1.26 (0.19), residues: 756 sheet: 0.56 (0.61), residues: 72 loop : -0.67 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.005 0.001 HIS A 27 PHE 0.014 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.003 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.403 Fit side-chains REVERT: D 304 LYS cc_start: 0.7815 (mttt) cc_final: 0.7288 (mmtt) REVERT: C 272 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8743 (m) REVERT: E 325 GLU cc_start: 0.7981 (pt0) cc_final: 0.7630 (pt0) REVERT: A 96 GLU cc_start: 0.7699 (tt0) cc_final: 0.7365 (tt0) REVERT: A 137 LYS cc_start: 0.7840 (tttt) cc_final: 0.7594 (ttmm) REVERT: A 149 ARG cc_start: 0.7272 (mmt-90) cc_final: 0.6876 (mmt90) REVERT: A 520 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8174 (ttpp) REVERT: A 543 LYS cc_start: 0.7713 (ptpt) cc_final: 0.7325 (mttt) REVERT: A 776 GLU cc_start: 0.7565 (tt0) cc_final: 0.7223 (mm-30) REVERT: A 826 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8162 (mtpt) REVERT: A 896 GLN cc_start: 0.7168 (mp10) cc_final: 0.6649 (mm110) REVERT: A 956 MET cc_start: 0.8835 (tpt) cc_final: 0.8614 (tpp) REVERT: A 1042 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7753 (ttp) REVERT: A 1052 GLN cc_start: 0.8300 (tt0) cc_final: 0.8092 (mt0) REVERT: A 1090 MET cc_start: 0.8222 (mmm) cc_final: 0.8003 (tpt) REVERT: A 1111 MET cc_start: 0.7959 (mtp) cc_final: 0.7757 (mtt) REVERT: A 1133 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7915 (mmtp) REVERT: A 1249 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8435 (pp) REVERT: A 1317 MET cc_start: 0.7453 (mtm) cc_final: 0.7205 (mtp) REVERT: A 1331 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8633 (t) REVERT: A 1334 LYS cc_start: 0.7803 (mttt) cc_final: 0.7027 (mptt) REVERT: A 1340 THR cc_start: 0.7202 (p) cc_final: 0.6901 (m) outliers start: 34 outliers final: 24 residues processed: 190 average time/residue: 1.2313 time to fit residues: 254.6084 Evaluate side-chains 200 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 7.9990 chunk 137 optimal weight: 0.0870 chunk 141 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 974 ASN A1314 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12420 Z= 0.245 Angle : 0.542 12.972 16818 Z= 0.268 Chirality : 0.043 0.156 1939 Planarity : 0.004 0.039 2144 Dihedral : 4.356 45.925 1668 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.42 (0.22), residues: 1526 helix: 1.10 (0.19), residues: 761 sheet: 0.57 (0.61), residues: 72 loop : -0.63 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 169 HIS 0.010 0.001 HIS A 475 PHE 0.015 0.001 PHE A 396 TYR 0.012 0.001 TYR A 283 ARG 0.008 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.407 Fit side-chains REVERT: D 304 LYS cc_start: 0.7837 (mttt) cc_final: 0.7458 (mptt) REVERT: C 272 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 282 MET cc_start: 0.6767 (mmt) cc_final: 0.6548 (mmt) REVERT: E 325 GLU cc_start: 0.7973 (pt0) cc_final: 0.7608 (pt0) REVERT: A 96 GLU cc_start: 0.7605 (tt0) cc_final: 0.7335 (tt0) REVERT: A 137 LYS cc_start: 0.7842 (tttt) cc_final: 0.7568 (ttmm) REVERT: A 149 ARG cc_start: 0.7274 (mmt-90) cc_final: 0.6891 (mmt90) REVERT: A 277 ASP cc_start: 0.8034 (p0) cc_final: 0.7760 (p0) REVERT: A 520 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8189 (ttpp) REVERT: A 543 LYS cc_start: 0.7766 (ptpt) cc_final: 0.7395 (mttt) REVERT: A 776 GLU cc_start: 0.7578 (tt0) cc_final: 0.7235 (mm-30) REVERT: A 826 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8205 (mtpt) REVERT: A 896 GLN cc_start: 0.7244 (mp10) cc_final: 0.6679 (mm110) REVERT: A 956 MET cc_start: 0.8813 (tpt) cc_final: 0.8580 (tpp) REVERT: A 1042 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7749 (ttp) REVERT: A 1090 MET cc_start: 0.8270 (mmm) cc_final: 0.8048 (tpt) REVERT: A 1133 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.7898 (mmtp) REVERT: A 1249 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8512 (pp) REVERT: A 1317 MET cc_start: 0.7498 (mtm) cc_final: 0.7240 (mtp) REVERT: A 1331 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8565 (t) REVERT: A 1340 THR cc_start: 0.7333 (p) cc_final: 0.7016 (m) outliers start: 35 outliers final: 22 residues processed: 188 average time/residue: 1.2637 time to fit residues: 258.5865 Evaluate side-chains 193 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 197 ASN A 463 ASN A 475 HIS A1314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12420 Z= 0.147 Angle : 0.488 12.715 16818 Z= 0.242 Chirality : 0.040 0.145 1939 Planarity : 0.004 0.038 2144 Dihedral : 4.160 42.547 1668 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.20 % Allowed : 17.14 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.22), residues: 1526 helix: 1.34 (0.19), residues: 756 sheet: 0.54 (0.58), residues: 76 loop : -0.55 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1227 HIS 0.005 0.001 HIS A 27 PHE 0.014 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.007 0.000 ARG A1189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.583 Fit side-chains REVERT: D 304 LYS cc_start: 0.7812 (mttt) cc_final: 0.7280 (mmtt) REVERT: C 272 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8748 (m) REVERT: B 282 MET cc_start: 0.6782 (mmt) cc_final: 0.6563 (mmt) REVERT: E 325 GLU cc_start: 0.7955 (pt0) cc_final: 0.7591 (pt0) REVERT: A 96 GLU cc_start: 0.7673 (tt0) cc_final: 0.7342 (tt0) REVERT: A 137 LYS cc_start: 0.7847 (tttt) cc_final: 0.7601 (ttmm) REVERT: A 520 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8162 (ttpp) REVERT: A 543 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7388 (mttt) REVERT: A 776 GLU cc_start: 0.7565 (tt0) cc_final: 0.7222 (mm-30) REVERT: A 826 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8157 (mtpt) REVERT: A 896 GLN cc_start: 0.7177 (mp10) cc_final: 0.6646 (mm110) REVERT: A 956 MET cc_start: 0.8830 (tpt) cc_final: 0.8517 (tpp) REVERT: A 1042 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: A 1052 GLN cc_start: 0.8308 (tt0) cc_final: 0.8086 (mt0) REVERT: A 1090 MET cc_start: 0.8223 (mmm) cc_final: 0.7992 (tpt) REVERT: A 1111 MET cc_start: 0.8093 (mtp) cc_final: 0.7853 (mtt) REVERT: A 1123 ARG cc_start: 0.8607 (ttt-90) cc_final: 0.8382 (ttt-90) REVERT: A 1133 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7889 (mmtp) REVERT: A 1249 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8523 (pp) REVERT: A 1334 LYS cc_start: 0.7487 (mttt) cc_final: 0.7278 (tppt) REVERT: A 1340 THR cc_start: 0.7187 (p) cc_final: 0.6881 (m) outliers start: 30 outliers final: 20 residues processed: 185 average time/residue: 1.2222 time to fit residues: 245.6786 Evaluate side-chains 192 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 826 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 HIS A 78 GLN A 463 ASN A 475 HIS A 749 GLN A1314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100487 restraints weight = 32580.689| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.38 r_work: 0.2784 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12420 Z= 0.112 Angle : 0.469 11.913 16818 Z= 0.233 Chirality : 0.039 0.142 1939 Planarity : 0.003 0.038 2144 Dihedral : 3.983 38.625 1668 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.54 % Allowed : 18.10 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.88 (0.22), residues: 1526 helix: 1.56 (0.20), residues: 754 sheet: 0.51 (0.56), residues: 76 loop : -0.46 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1227 HIS 0.004 0.001 HIS A 475 PHE 0.015 0.001 PHE A 396 TYR 0.011 0.001 TYR A 908 ARG 0.007 0.000 ARG A1189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4789.35 seconds wall clock time: 85 minutes 17.79 seconds (5117.79 seconds total)