Starting phenix.real_space_refine on Sun Mar 24 04:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/03_2024/6f0k_4165_trim_updated.pdb" } resolution = 3.87 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= 0.006 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 Fe 21 7.16 5 S 102 5.16 5 C 13192 2.51 5 N 3475 2.21 5 O 3501 1.98 5 H 19577 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 171": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 201": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 268": not complete - not flipped Residue "B ARG 278": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 285": not complete - not flipped Residue "B ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 521": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 640": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 706": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 751": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 795": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 835": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 844": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 912": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 940": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 952": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 965": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1024": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" Residue "E ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 264": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 399": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39868 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3253 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "B" Number of atoms: 14877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 14877 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 69, 'TRANS': 891} Chain: "C" Number of atoms: 7234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 7234 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2656 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 13, 'TRANS': 157} Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2818 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 16, 'TRANS': 165} Chain: "F" Number of atoms: 6308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 6308 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain: "H" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2433 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15587 SG CYS B 877 85.250 70.092 49.180 1.00 58.24 S ATOM 15972 SG CYS B 903 88.185 72.952 48.056 1.00 54.69 S ATOM 15877 SG CYS B 897 87.771 68.752 44.076 1.00 52.19 S ATOM 15972 SG CYS B 903 88.185 72.952 48.056 1.00 54.69 S ATOM 15428 SG CYS B 865 97.302 74.866 51.557 1.00 49.56 S ATOM 15535 SG CYS B 873 91.925 75.044 52.472 1.00 54.76 S ATOM 16021 SG CYS B 907 95.472 79.689 50.127 1.00 54.76 S ATOM 15472 SG CYS B 868 95.716 78.747 56.213 1.00 55.18 S ATOM 17190 SG CYS B 976 108.848 70.852 50.397 1.00 52.77 S ATOM 16742 SG CYS B 949 106.840 66.268 51.898 1.00 48.84 S ATOM 14681 SG CYS B 817 105.519 68.574 46.570 1.00 52.91 S ATOM 16697 SG CYS B 946 103.020 70.967 52.034 1.00 49.60 S ATOM 14592 SG CYS B 810 117.426 73.883 46.826 1.00 59.01 S ATOM 17244 SG CYS B 980 116.557 73.998 52.083 1.00 54.49 S ATOM 14626 SG CYS B 813 113.156 73.802 50.004 1.00 54.79 S ATOM 14561 SG CYS B 807 114.424 79.058 50.646 1.00 61.36 S Time building chain proxies: 15.68, per 1000 atoms: 0.39 Number of scatterers: 39868 At special positions: 0 Unit cell: (165.6, 136.62, 105.57, 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) Fe 21 26.01 S 102 16.00 O 3501 8.00 N 3475 7.00 C 13192 6.00 H 19577 1.00 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.61 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1101 " pdb="FE1 F3S B1101 " - pdb=" SG CYS B 877 " pdb="FE4 F3S B1101 " - pdb=" SG CYS B 903 " pdb="FE3 F3S B1101 " - pdb=" SG CYS B 897 " pdb=" SF4 B1102 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 865 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 868 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 907 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 873 " pdb=" SF4 B1103 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 976 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 949 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 946 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 817 " pdb=" SF4 B1104 " pdb="FE3 SF4 B1104 " - pdb=" SG CYS B 813 " pdb="FE1 SF4 B1104 " - pdb=" SG CYS B 810 " pdb="FE2 SF4 B1104 " - pdb=" SG CYS B 980 " pdb="FE4 SF4 B1104 " - pdb=" SG CYS B 807 " Number of angles added : 45 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4682 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 3 sheets defined 42.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 30 removed outlier: 3.506A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.340A pdb=" N ASN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.769A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.698A pdb=" N GLN B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.619A pdb=" N ARG B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.930A pdb=" N GLU B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.568A pdb=" N ALA B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.845A pdb=" N ILE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.539A pdb=" N VAL B 372 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 373 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.591A pdb=" N ALA B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 4.160A pdb=" N GLN B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.884A pdb=" N ALA B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 521 removed outlier: 3.710A pdb=" N ARG B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 4.721A pdb=" N GLN B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 592 No H-bonds generated for 'chain 'B' and resid 589 through 592' Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 786 through 789 No H-bonds generated for 'chain 'B' and resid 786 through 789' Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 815 through 820 Processing helix chain 'B' and resid 828 through 833 removed outlier: 4.969A pdb=" N ARG B 833 " --> pdb=" O ASN B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 No H-bonds generated for 'chain 'B' and resid 902 through 905' Processing helix chain 'B' and resid 927 through 929 No H-bonds generated for 'chain 'B' and resid 927 through 929' Processing helix chain 'B' and resid 947 through 962 removed outlier: 5.716A pdb=" N GLN B 951 " --> pdb=" O TYR B 948 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU B 955 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 958 " --> pdb=" O GLU B 955 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 962 " --> pdb=" O GLN B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 979 Processing helix chain 'B' and resid 996 through 1002 Processing helix chain 'B' and resid 1011 through 1013 No H-bonds generated for 'chain 'B' and resid 1011 through 1013' Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.648A pdb=" N LEU C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 67 removed outlier: 3.794A pdb=" N SER C 50 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.625A pdb=" N SER C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 118 through 136 removed outlier: 4.390A pdb=" N GLU C 122 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE C 127 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE C 134 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 165 through 201 removed outlier: 3.780A pdb=" N VAL C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Proline residue: C 190 - end of helix removed outlier: 4.138A pdb=" N ALA C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 222 through 255 removed outlier: 4.644A pdb=" N ASN C 227 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Proline residue: C 241 - end of helix removed outlier: 3.595A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 No H-bonds generated for 'chain 'C' and resid 260 through 263' Processing helix chain 'C' and resid 265 through 289 Proline residue: C 268 - end of helix removed outlier: 3.761A pdb=" N PHE C 271 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE C 280 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 288 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 329 removed outlier: 3.982A pdb=" N ILE C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 312 " --> pdb=" O MET C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.815A pdb=" N PHE C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 366 removed outlier: 4.295A pdb=" N TRP C 352 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 354 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP C 355 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET C 358 " --> pdb=" O TRP C 355 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 363 " --> pdb=" O CYS C 360 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE C 364 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Proline residue: C 365 - end of helix Processing helix chain 'C' and resid 378 through 398 removed outlier: 3.670A pdb=" N ILE C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 442 removed outlier: 3.877A pdb=" N LEU C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 454 removed outlier: 3.789A pdb=" N LYS C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.868A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 42 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 94 removed outlier: 4.670A pdb=" N THR D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 Proline residue: D 118 - end of helix Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.757A pdb=" N ALA D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'E' and resid 78 through 81 No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 100 through 113 removed outlier: 3.520A pdb=" N ARG E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 130 No H-bonds generated for 'chain 'E' and resid 127 through 130' Processing helix chain 'E' and resid 144 through 147 No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.688A pdb=" N ILE E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 190 removed outlier: 4.033A pdb=" N VAL E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'F' and resid 39 through 56 removed outlier: 4.476A pdb=" N VAL F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 89 removed outlier: 3.582A pdb=" N TYR F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 100 through 125 removed outlier: 4.351A pdb=" N TRP F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix removed outlier: 4.006A pdb=" N VAL F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) Proline residue: F 118 - end of helix removed outlier: 3.589A pdb=" N PHE F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 122 " --> pdb=" O PRO F 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 3.710A pdb=" N VAL F 160 " --> pdb=" O PRO F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 169 through 180 removed outlier: 3.752A pdb=" N ALA F 173 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR F 178 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 203 through 217 removed outlier: 3.792A pdb=" N GLY F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 253 removed outlier: 4.275A pdb=" N PHE F 234 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 236 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY F 237 " --> pdb=" O PHE F 234 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE F 240 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA F 242 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 243 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 246 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 248 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS F 249 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 288 removed outlier: 3.544A pdb=" N ASP F 270 " --> pdb=" O PRO F 266 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 281 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE F 285 " --> pdb=" O PHE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 removed outlier: 3.571A pdb=" N GLY F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.603A pdb=" N LEU F 303 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR F 305 " --> pdb=" O THR F 302 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG F 306 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS F 307 " --> pdb=" O TRP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 324 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 341 through 359 removed outlier: 3.646A pdb=" N ILE F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE F 354 " --> pdb=" O TRP F 350 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE F 357 " --> pdb=" O ILE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 removed outlier: 3.602A pdb=" N HIS F 368 " --> pdb=" O PRO F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 399 removed outlier: 3.806A pdb=" N THR F 380 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS F 381 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 383 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 385 " --> pdb=" O TRP F 382 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 386 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL F 389 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG F 396 " --> pdb=" O PHE F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 414 Processing helix chain 'H' and resid 33 through 60 removed outlier: 3.584A pdb=" N GLU H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 75 removed outlier: 4.179A pdb=" N ALA H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 74 " --> pdb=" O TYR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 96 removed outlier: 3.769A pdb=" N LEU H 86 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 95 " --> pdb=" O TRP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 134 removed outlier: 6.281A pdb=" N ASN H 106 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG H 107 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 109 " --> pdb=" O ASN H 106 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR H 113 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA H 118 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP H 128 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA H 129 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 134 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 157 through 167 removed outlier: 3.868A pdb=" N GLN H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing sheet with id= A, first strand: chain 'B' and resid 102 through 105 Processing sheet with id= B, first strand: chain 'B' and resid 415 through 417 Processing sheet with id= C, first strand: chain 'B' and resid 471 through 473 removed outlier: 3.748A pdb=" N GLY B 472 " --> pdb=" O SER B 480 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1257 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: 14.05 Time building geometry restraints manager: 31.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.42: 28741 1.42 - 2.02: 11750 2.02 - 2.61: 49 2.61 - 3.21: 0 3.21 - 3.81: 3 Bond restraints: 40543 Sorted by residual: bond pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " ideal model delta sigma weight residual 2.258 3.812 -1.554 2.00e-02 2.50e+03 6.04e+03 bond pdb=" S4 F3S B1101 " pdb="FE1 F3S B1101 " ideal model delta sigma weight residual 2.233 3.763 -1.530 2.00e-02 2.50e+03 5.86e+03 bond pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 2.300 3.809 -1.509 2.00e-02 2.50e+03 5.69e+03 bond pdb=" CAB HEC A 301 " pdb=" CBB HEC A 301 " ideal model delta sigma weight residual 1.544 1.308 0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" CAB HEC A 302 " pdb=" CBB HEC A 302 " ideal model delta sigma weight residual 1.544 1.315 0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 40538 not shown) Histogram of bond angle deviations from ideal: 36.95 - 65.17: 4 65.17 - 93.39: 79 93.39 - 121.61: 64620 121.61 - 149.83: 8417 149.83 - 178.04: 12 Bond angle restraints: 73132 Sorted by residual: angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S3 F3S B1101 " ideal model delta sigma weight residual 114.75 68.18 46.57 3.00e+00 1.11e-01 2.41e+02 angle pdb=" S3 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 112.59 70.67 41.92 3.00e+00 1.11e-01 1.95e+02 angle pdb=" CA CYS A 206 " pdb=" CB CYS A 206 " pdb=" SG CYS A 206 " ideal model delta sigma weight residual 114.40 85.29 29.11 2.30e+00 1.89e-01 1.60e+02 angle pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 74.86 38.28 36.58 3.00e+00 1.11e-01 1.49e+02 angle pdb="FE1 F3S B1101 " pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 72.09 36.95 35.14 3.00e+00 1.11e-01 1.37e+02 ... (remaining 73127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 18739 35.93 - 71.86: 343 71.86 - 107.80: 22 107.80 - 143.73: 0 143.73 - 179.66: 2 Dihedral angle restraints: 19106 sinusoidal: 10060 harmonic: 9046 Sorted by residual: dihedral pdb=" CD ARG B 268 " pdb=" NE ARG B 268 " pdb=" CZ ARG B 268 " pdb=" NH1 ARG B 268 " ideal model delta sinusoidal sigma weight residual 0.00 179.66 -179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG B 285 " pdb=" NE ARG B 285 " pdb=" CZ ARG B 285 " pdb=" NH1 ARG B 285 " ideal model delta sinusoidal sigma weight residual 0.00 179.66 -179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C2C HEC A 301 " pdb=" C3C HEC A 301 " pdb=" CAC HEC A 301 " pdb=" CBC HEC A 301 " ideal model delta sinusoidal sigma weight residual 60.00 -25.00 85.00 2 1.00e+01 1.00e-02 4.76e+01 ... (remaining 19103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.130: 3057 1.130 - 2.260: 4 2.260 - 3.391: 0 3.391 - 4.521: 0 4.521 - 5.651: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb="FE3 F3S B1101 " pdb="FE4 F3S B1101 " both_signs ideal model delta sigma weight residual False 10.77 5.12 5.65 2.00e-01 2.50e+01 7.98e+02 chirality pdb=" CG LEU F 327 " pdb=" CB LEU F 327 " pdb=" CD1 LEU F 327 " pdb=" CD2 LEU F 327 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.07e+01 chirality pdb=" CG LEU F 303 " pdb=" CB LEU F 303 " pdb=" CD1 LEU F 303 " pdb=" CD2 LEU F 303 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.92e+01 ... (remaining 3059 not shown) Planarity restraints: 5986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEC A 301 " 0.014 2.00e-02 2.50e+03 4.80e-02 5.18e+01 pdb=" C1B HEC A 301 " 0.014 2.00e-02 2.50e+03 pdb=" C2B HEC A 301 " -0.018 2.00e-02 2.50e+03 pdb=" C3B HEC A 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4B HEC A 301 " -0.013 2.00e-02 2.50e+03 pdb=" CAB HEC A 301 " 0.094 2.00e-02 2.50e+03 pdb=" CHB HEC A 301 " 0.054 2.00e-02 2.50e+03 pdb=" CHC HEC A 301 " -0.049 2.00e-02 2.50e+03 pdb=" CMB HEC A 301 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " -0.001 2.00e-02 2.50e+03 3.46e-02 2.69e+01 pdb=" C2C HEC A 303 " 0.017 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " -0.062 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " -0.044 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " 0.033 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.059 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 305 " -0.008 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" C2C HEC A 305 " 0.027 2.00e-02 2.50e+03 pdb=" C3C HEC A 305 " 0.004 2.00e-02 2.50e+03 pdb=" C4C HEC A 305 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC A 305 " -0.054 2.00e-02 2.50e+03 pdb=" CHC HEC A 305 " -0.028 2.00e-02 2.50e+03 pdb=" CHD HEC A 305 " 0.031 2.00e-02 2.50e+03 pdb=" CMC HEC A 305 " 0.039 2.00e-02 2.50e+03 pdb=" NC HEC A 305 " -0.015 2.00e-02 2.50e+03 ... (remaining 5983 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 764 2.10 - 2.73: 71181 2.73 - 3.35: 117371 3.35 - 3.98: 147376 3.98 - 4.60: 234625 Nonbonded interactions: 571317 Sorted by model distance: nonbonded pdb=" O THR B 808 " pdb="HG22 THR B 808 " model vdw 1.480 2.620 nonbonded pdb="HG22 VAL B 295 " pdb="HG22 THR B 808 " model vdw 1.580 2.440 nonbonded pdb="HH12 ARG B 901 " pdb=" O HIS C 139 " model vdw 1.638 1.850 nonbonded pdb=" O ASN F 154 " pdb=" H PHE F 157 " model vdw 1.645 1.850 nonbonded pdb=" O ASN B 588 " pdb=" H GLN B 592 " model vdw 1.663 1.850 ... (remaining 571312 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: 1.410 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: 0.580 Extract box with map and model: 7.260 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 126.420 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.022 1.554 20966 Z= 1.378 Angle : 1.288 46.572 28742 Z= 0.598 Chirality : 0.138 5.651 3062 Planarity : 0.008 0.077 3661 Dihedral : 11.891 179.659 7377 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -5.22 (0.14), residues: 2490 helix: -3.63 (0.11), residues: 991 sheet: -5.50 (0.32), residues: 72 loop : -3.34 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 74 HIS 0.019 0.003 HIS F 307 PHE 0.032 0.003 PHE C 267 TYR 0.039 0.003 TYR A 48 ARG 0.025 0.002 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 638 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4570 (ttm170) cc_final: 0.4283 (mmt180) REVERT: A 88 GLN cc_start: 0.7570 (pt0) cc_final: 0.6339 (tm-30) REVERT: A 119 ASP cc_start: 0.8094 (t0) cc_final: 0.7797 (m-30) REVERT: B 154 SER cc_start: 0.8132 (p) cc_final: 0.7859 (p) REVERT: B 598 ILE cc_start: 0.8956 (mm) cc_final: 0.8591 (mt) REVERT: B 820 GLU cc_start: 0.7522 (tp30) cc_final: 0.7275 (tp30) REVERT: B 1019 THR cc_start: 0.7189 (t) cc_final: 0.6456 (m) REVERT: C 318 MET cc_start: 0.7121 (tpt) cc_final: 0.6831 (mmt) REVERT: C 340 TYR cc_start: 0.7791 (t80) cc_final: 0.7518 (t80) REVERT: C 354 TYR cc_start: 0.7653 (t80) cc_final: 0.7247 (t80) REVERT: C 394 GLU cc_start: 0.6838 (tt0) cc_final: 0.5948 (tt0) REVERT: D 45 LYS cc_start: 0.8691 (mttt) cc_final: 0.8478 (mtmt) REVERT: D 59 ILE cc_start: 0.7615 (pt) cc_final: 0.7342 (pt) REVERT: D 175 ASP cc_start: 0.7503 (m-30) cc_final: 0.6598 (p0) REVERT: E 51 LEU cc_start: 0.8492 (tp) cc_final: 0.7656 (tp) REVERT: E 159 SER cc_start: 0.8394 (m) cc_final: 0.7760 (t) REVERT: F 175 LYS cc_start: 0.6856 (ttmm) cc_final: 0.6517 (mmtt) REVERT: F 182 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7269 (mmt180) REVERT: F 196 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.6764 (ttt-90) REVERT: F 270 ASP cc_start: 0.8122 (m-30) cc_final: 0.7234 (t70) REVERT: F 329 PHE cc_start: 0.8153 (t80) cc_final: 0.7896 (t80) REVERT: H 73 GLN cc_start: 0.6870 (tt0) cc_final: 0.6381 (tt0) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.9217 time to fit residues: 836.5180 Evaluate side-chains 381 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 0.0060 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.0050 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 144 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN B 408 GLN B 592 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS H 121 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 20966 Z= 0.249 Angle : 0.954 89.976 28742 Z= 0.428 Chirality : 0.078 1.749 3062 Planarity : 0.007 0.073 3661 Dihedral : 9.867 179.345 2816 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 1.35 % Allowed : 9.43 % Favored : 89.23 % 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: -4.63 (0.14), residues: 2490 helix: -2.80 (0.12), residues: 1046 sheet: -5.38 (0.32), residues: 83 loop : -3.22 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 562 HIS 0.013 0.002 HIS F 371 PHE 0.032 0.002 PHE D 79 TYR 0.029 0.002 TYR B 902 ARG 0.007 0.001 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 449 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 421 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4591 (ttm170) cc_final: 0.4246 (mmt180) REVERT: B 91 ILE cc_start: 0.8314 (pt) cc_final: 0.7773 (mp) REVERT: B 608 ILE cc_start: 0.8266 (mp) cc_final: 0.7909 (mt) REVERT: B 978 GLN cc_start: 0.7766 (tt0) cc_final: 0.7533 (tt0) REVERT: C 92 TRP cc_start: 0.7590 (m100) cc_final: 0.7238 (m100) REVERT: C 340 TYR cc_start: 0.7672 (t80) cc_final: 0.7368 (t80) REVERT: C 388 ASN cc_start: 0.8499 (t0) cc_final: 0.8278 (t0) REVERT: D 45 LYS cc_start: 0.8798 (mttt) cc_final: 0.8587 (mtmt) REVERT: F 196 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.6035 (ttt-90) REVERT: H 55 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7241 (tp30) outliers start: 28 outliers final: 15 residues processed: 438 average time/residue: 0.8062 time to fit residues: 527.4090 Evaluate side-chains 371 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 356 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 367 PHE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN B 408 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 20966 Z= 0.516 Angle : 1.009 80.676 28742 Z= 0.468 Chirality : 0.085 1.814 3062 Planarity : 0.007 0.076 3661 Dihedral : 9.532 180.000 2816 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.02 % Favored : 83.98 % Rotamer: Outliers : 2.31 % Allowed : 11.78 % Favored : 85.91 % 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: -4.75 (0.14), residues: 2490 helix: -2.70 (0.12), residues: 1057 sheet: -5.47 (0.32), residues: 83 loop : -3.47 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 562 HIS 0.019 0.002 HIS B 494 PHE 0.028 0.003 PHE D 111 TYR 0.036 0.003 TYR B 909 ARG 0.007 0.001 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 365 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4915 (ttm170) cc_final: 0.4326 (mmt-90) REVERT: B 407 MET cc_start: 0.8278 (mmt) cc_final: 0.7906 (mmt) REVERT: B 818 ASP cc_start: 0.7927 (m-30) cc_final: 0.7713 (m-30) REVERT: B 820 GLU cc_start: 0.7780 (tp30) cc_final: 0.7209 (tp30) REVERT: B 823 ILE cc_start: 0.8245 (pt) cc_final: 0.7758 (pt) REVERT: B 925 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7927 (pt) REVERT: C 209 LYS cc_start: 0.7804 (tttt) cc_final: 0.6948 (ttpt) REVERT: C 340 TYR cc_start: 0.8217 (t80) cc_final: 0.7847 (t80) REVERT: D 48 TYR cc_start: 0.5248 (p90) cc_final: 0.4980 (p90) REVERT: D 60 HIS cc_start: 0.8026 (m90) cc_final: 0.7310 (t70) REVERT: E 31 LYS cc_start: 0.7923 (mmpt) cc_final: 0.7206 (tttm) REVERT: E 159 SER cc_start: 0.8603 (m) cc_final: 0.8062 (t) REVERT: E 176 ASP cc_start: 0.7922 (m-30) cc_final: 0.7564 (m-30) REVERT: F 196 ARG cc_start: 0.8270 (mmt-90) cc_final: 0.6151 (ttt-90) REVERT: F 270 ASP cc_start: 0.8420 (m-30) cc_final: 0.7553 (t0) outliers start: 48 outliers final: 35 residues processed: 394 average time/residue: 0.7323 time to fit residues: 437.8518 Evaluate side-chains 369 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 333 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 780 ASN Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20966 Z= 0.265 Angle : 0.877 80.726 28742 Z= 0.390 Chirality : 0.080 1.750 3062 Planarity : 0.006 0.074 3661 Dihedral : 9.103 179.457 2816 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 2.12 % Allowed : 12.94 % Favored : 84.94 % 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: -4.27 (0.15), residues: 2490 helix: -2.35 (0.13), residues: 1067 sheet: -5.37 (0.32), residues: 74 loop : -3.18 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 562 HIS 0.008 0.001 HIS C 247 PHE 0.027 0.002 PHE D 111 TYR 0.018 0.001 TYR B1021 ARG 0.006 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 363 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.5016 (ttm170) cc_final: 0.4614 (mmt180) REVERT: A 119 ASP cc_start: 0.7740 (m-30) cc_final: 0.7372 (t0) REVERT: B 407 MET cc_start: 0.8133 (mmt) cc_final: 0.7815 (mmt) REVERT: B 823 ILE cc_start: 0.8301 (pt) cc_final: 0.7831 (pt) REVERT: B 1009 MET cc_start: 0.8172 (tpp) cc_final: 0.7726 (tpp) REVERT: C 92 TRP cc_start: 0.8049 (m100) cc_final: 0.7633 (m100) REVERT: C 209 LYS cc_start: 0.7663 (tttt) cc_final: 0.6834 (pttp) REVERT: C 340 TYR cc_start: 0.8092 (t80) cc_final: 0.7736 (t80) REVERT: D 60 HIS cc_start: 0.7902 (m90) cc_final: 0.6992 (t70) REVERT: E 31 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7189 (tttm) REVERT: F 196 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.6089 (ttt-90) REVERT: F 219 MET cc_start: 0.6675 (tpt) cc_final: 0.6336 (tpt) REVERT: F 270 ASP cc_start: 0.8425 (m-30) cc_final: 0.7542 (t0) outliers start: 44 outliers final: 32 residues processed: 385 average time/residue: 0.7492 time to fit residues: 446.4949 Evaluate side-chains 372 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 340 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 20966 Z= 0.354 Angle : 0.891 80.313 28742 Z= 0.399 Chirality : 0.081 1.800 3062 Planarity : 0.006 0.069 3661 Dihedral : 8.980 179.985 2816 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Rotamer: Outliers : 2.74 % Allowed : 13.80 % Favored : 83.45 % 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: -4.17 (0.15), residues: 2490 helix: -2.17 (0.14), residues: 1067 sheet: -5.36 (0.35), residues: 74 loop : -3.21 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 562 HIS 0.012 0.001 HIS C 247 PHE 0.028 0.002 PHE D 111 TYR 0.031 0.002 TYR B 909 ARG 0.006 0.000 ARG B 705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 345 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.5143 (ttm170) cc_final: 0.4799 (mmt180) REVERT: B 407 MET cc_start: 0.8202 (mmt) cc_final: 0.7913 (mmt) REVERT: B 503 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 808 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6204 (t) REVERT: B 1009 MET cc_start: 0.8223 (tpp) cc_final: 0.7736 (tpp) REVERT: C 92 TRP cc_start: 0.8075 (m100) cc_final: 0.7657 (m100) REVERT: C 209 LYS cc_start: 0.7736 (tttt) cc_final: 0.6905 (pttp) REVERT: C 340 TYR cc_start: 0.8202 (t80) cc_final: 0.7870 (t80) REVERT: D 60 HIS cc_start: 0.7967 (m90) cc_final: 0.7109 (t70) REVERT: E 31 LYS cc_start: 0.7914 (mmpt) cc_final: 0.7243 (tttm) REVERT: F 196 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.6169 (ttt-90) REVERT: F 219 MET cc_start: 0.6726 (tpt) cc_final: 0.6340 (tpt) REVERT: F 270 ASP cc_start: 0.8516 (m-30) cc_final: 0.7615 (t0) outliers start: 57 outliers final: 45 residues processed: 376 average time/residue: 0.6997 time to fit residues: 405.9110 Evaluate side-chains 380 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 333 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 20966 Z= 0.326 Angle : 0.877 80.442 28742 Z= 0.390 Chirality : 0.081 1.816 3062 Planarity : 0.006 0.071 3661 Dihedral : 8.797 179.589 2816 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 2.79 % Allowed : 14.48 % Favored : 82.73 % 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: -3.98 (0.15), residues: 2490 helix: -2.00 (0.14), residues: 1071 sheet: -5.07 (0.39), residues: 79 loop : -3.12 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 562 HIS 0.010 0.001 HIS B 494 PHE 0.027 0.002 PHE D 111 TYR 0.041 0.002 TYR B 902 ARG 0.008 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 347 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4968 (ttm170) cc_final: 0.4710 (mmt180) REVERT: A 119 ASP cc_start: 0.8033 (m-30) cc_final: 0.7492 (t0) REVERT: B 503 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8877 (mm) REVERT: B 512 TYR cc_start: 0.7808 (t80) cc_final: 0.7385 (t80) REVERT: B 808 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6458 (t) REVERT: C 26 PHE cc_start: 0.6302 (m-10) cc_final: 0.6058 (p90) REVERT: C 92 TRP cc_start: 0.8127 (m100) cc_final: 0.7705 (m100) REVERT: C 209 LYS cc_start: 0.7820 (tttt) cc_final: 0.6898 (pttp) REVERT: C 340 TYR cc_start: 0.8205 (t80) cc_final: 0.7894 (t80) REVERT: D 60 HIS cc_start: 0.7893 (m90) cc_final: 0.6983 (t70) REVERT: D 94 TRP cc_start: 0.5721 (t-100) cc_final: 0.5493 (t-100) REVERT: D 156 MET cc_start: 0.5319 (mtm) cc_final: 0.4909 (ttm) REVERT: E 31 LYS cc_start: 0.7952 (mmpt) cc_final: 0.7294 (tttm) REVERT: F 196 ARG cc_start: 0.8167 (mmt-90) cc_final: 0.6078 (tmt170) REVERT: F 219 MET cc_start: 0.6856 (tpt) cc_final: 0.6495 (tpt) REVERT: F 270 ASP cc_start: 0.8533 (m-30) cc_final: 0.7636 (t0) outliers start: 58 outliers final: 44 residues processed: 379 average time/residue: 0.7159 time to fit residues: 418.3653 Evaluate side-chains 386 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 340 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 20966 Z= 0.241 Angle : 0.847 80.390 28742 Z= 0.370 Chirality : 0.079 1.781 3062 Planarity : 0.005 0.062 3661 Dihedral : 8.562 179.658 2816 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 2.36 % Allowed : 15.87 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.68 (0.15), residues: 2490 helix: -1.73 (0.15), residues: 1072 sheet: -4.78 (0.41), residues: 84 loop : -2.97 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 382 HIS 0.010 0.001 HIS C 247 PHE 0.026 0.002 PHE D 111 TYR 0.033 0.001 TYR B 902 ARG 0.006 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 359 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.4944 (ttm170) cc_final: 0.4738 (mmt180) REVERT: A 152 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 512 TYR cc_start: 0.7764 (t80) cc_final: 0.7355 (t80) REVERT: B 808 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6483 (t) REVERT: B 847 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7865 (m) REVERT: B 1009 MET cc_start: 0.8213 (tpp) cc_final: 0.7853 (tpp) REVERT: C 26 PHE cc_start: 0.6298 (m-10) cc_final: 0.6031 (p90) REVERT: C 92 TRP cc_start: 0.8078 (m100) cc_final: 0.7688 (m100) REVERT: C 209 LYS cc_start: 0.7863 (tttt) cc_final: 0.6955 (pttp) REVERT: C 340 TYR cc_start: 0.8121 (t80) cc_final: 0.7808 (t80) REVERT: D 60 HIS cc_start: 0.7879 (m90) cc_final: 0.6901 (t70) REVERT: E 31 LYS cc_start: 0.7946 (mmpt) cc_final: 0.7312 (tttm) REVERT: E 44 GLU cc_start: 0.4171 (mm-30) cc_final: 0.3872 (mm-30) REVERT: F 196 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.6050 (tmt170) REVERT: F 219 MET cc_start: 0.6992 (tpt) cc_final: 0.6565 (tpt) REVERT: F 270 ASP cc_start: 0.8493 (m-30) cc_final: 0.7592 (t0) outliers start: 49 outliers final: 41 residues processed: 383 average time/residue: 0.6466 time to fit residues: 380.1545 Evaluate side-chains 381 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 338 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 271 PHE Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20966 Z= 0.265 Angle : 0.850 80.491 28742 Z= 0.371 Chirality : 0.079 1.787 3062 Planarity : 0.005 0.065 3661 Dihedral : 8.458 179.796 2816 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 2.31 % Allowed : 16.45 % Favored : 81.24 % 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: -3.55 (0.16), residues: 2490 helix: -1.61 (0.15), residues: 1066 sheet: -4.57 (0.45), residues: 79 loop : -2.93 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 562 HIS 0.012 0.001 HIS C 247 PHE 0.033 0.002 PHE F 278 TYR 0.023 0.001 TYR B 902 ARG 0.010 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 342 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8013 (m-30) cc_final: 0.7546 (t0) REVERT: A 152 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 512 TYR cc_start: 0.7781 (t80) cc_final: 0.7367 (t80) REVERT: B 808 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6614 (t) REVERT: B 847 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7809 (m) REVERT: B 1009 MET cc_start: 0.8161 (tpp) cc_final: 0.7670 (tpp) REVERT: C 92 TRP cc_start: 0.8076 (m100) cc_final: 0.7694 (m100) REVERT: C 340 TYR cc_start: 0.8159 (t80) cc_final: 0.7828 (t80) REVERT: C 392 TRP cc_start: 0.8515 (t60) cc_final: 0.8226 (t60) REVERT: D 136 MET cc_start: 0.7894 (tpt) cc_final: 0.7508 (tpt) REVERT: E 31 LYS cc_start: 0.7917 (mmpt) cc_final: 0.7380 (tttm) REVERT: F 196 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.6067 (tmt170) REVERT: F 219 MET cc_start: 0.7037 (tpt) cc_final: 0.6613 (tpt) REVERT: F 270 ASP cc_start: 0.8432 (m-30) cc_final: 0.7596 (t0) REVERT: F 351 PHE cc_start: 0.8349 (t80) cc_final: 0.7920 (t80) outliers start: 48 outliers final: 43 residues processed: 367 average time/residue: 0.7071 time to fit residues: 402.3300 Evaluate side-chains 377 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 332 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 65 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 271 PHE Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.4980 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 chunk 201 optimal weight: 0.0870 chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 GLN ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS H 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 20966 Z= 0.197 Angle : 0.836 80.742 28742 Z= 0.359 Chirality : 0.078 1.768 3062 Planarity : 0.005 0.059 3661 Dihedral : 8.264 179.806 2816 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 1.78 % Allowed : 17.22 % Favored : 81.00 % 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: -3.26 (0.16), residues: 2490 helix: -1.32 (0.15), residues: 1080 sheet: -4.38 (0.46), residues: 79 loop : -2.83 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 225 HIS 0.010 0.001 HIS C 247 PHE 0.025 0.002 PHE D 111 TYR 0.020 0.001 TYR F 295 ARG 0.008 0.000 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 351 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7361 (t80) cc_final: 0.6958 (t80) REVERT: A 119 ASP cc_start: 0.7945 (m-30) cc_final: 0.7521 (t0) REVERT: A 152 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 512 TYR cc_start: 0.7808 (t80) cc_final: 0.7353 (t80) REVERT: B 929 MET cc_start: 0.8260 (mmp) cc_final: 0.8008 (mmp) REVERT: B 978 GLN cc_start: 0.7508 (tt0) cc_final: 0.7303 (tt0) REVERT: B 994 ASN cc_start: 0.7164 (t0) cc_final: 0.6857 (t0) REVERT: B 1009 MET cc_start: 0.8186 (tpp) cc_final: 0.7747 (tpp) REVERT: C 176 TYR cc_start: 0.8190 (t80) cc_final: 0.7944 (t80) REVERT: C 340 TYR cc_start: 0.7985 (t80) cc_final: 0.7655 (t80) REVERT: C 392 TRP cc_start: 0.8439 (t60) cc_final: 0.7995 (t60) REVERT: D 45 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8045 (mtpt) REVERT: D 136 MET cc_start: 0.7863 (tpt) cc_final: 0.7527 (tpt) REVERT: D 156 MET cc_start: 0.5043 (mtm) cc_final: 0.4480 (ttm) REVERT: E 31 LYS cc_start: 0.7905 (mmpt) cc_final: 0.7398 (tttm) REVERT: E 151 ASP cc_start: 0.8826 (m-30) cc_final: 0.8475 (t0) REVERT: F 196 ARG cc_start: 0.8111 (mmt-90) cc_final: 0.6008 (tmt170) REVERT: F 219 MET cc_start: 0.6958 (tpt) cc_final: 0.6496 (tpt) REVERT: F 270 ASP cc_start: 0.8337 (m-30) cc_final: 0.7551 (t0) REVERT: F 349 ILE cc_start: 0.9004 (mm) cc_final: 0.8634 (mt) REVERT: F 364 MET cc_start: 0.6762 (tmm) cc_final: 0.6506 (tmm) outliers start: 37 outliers final: 30 residues processed: 372 average time/residue: 0.6935 time to fit residues: 402.9171 Evaluate side-chains 357 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 327 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 196 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 20966 Z= 0.236 Angle : 0.849 80.573 28742 Z= 0.362 Chirality : 0.079 1.773 3062 Planarity : 0.005 0.061 3661 Dihedral : 8.187 179.974 2816 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 1.64 % Allowed : 17.65 % Favored : 80.71 % 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: -3.21 (0.16), residues: 2490 helix: -1.26 (0.15), residues: 1081 sheet: -4.34 (0.47), residues: 79 loop : -2.83 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 382 HIS 0.012 0.001 HIS C 247 PHE 0.026 0.002 PHE D 111 TYR 0.016 0.001 TYR F 295 ARG 0.009 0.000 ARG E 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 40 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue SER 207 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue TYR 216 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue SER 610 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue SER 164 is missing expected H atoms. Skipping. Residue TYR 323 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue TYR 48 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue TYR 168 is missing expected H atoms. Skipping. Residue TYR 177 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 330 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7400 (t80) cc_final: 0.6911 (t80) REVERT: A 152 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 512 TYR cc_start: 0.7791 (t80) cc_final: 0.7388 (t80) REVERT: B 929 MET cc_start: 0.8366 (mmp) cc_final: 0.8130 (mmp) REVERT: B 994 ASN cc_start: 0.7134 (t0) cc_final: 0.6827 (t0) REVERT: C 92 TRP cc_start: 0.8075 (m100) cc_final: 0.7722 (m100) REVERT: C 340 TYR cc_start: 0.8098 (t80) cc_final: 0.7746 (t80) REVERT: C 392 TRP cc_start: 0.8562 (t60) cc_final: 0.8047 (t60) REVERT: D 136 MET cc_start: 0.7873 (tpt) cc_final: 0.7545 (tpt) REVERT: D 156 MET cc_start: 0.4867 (mtm) cc_final: 0.4440 (ttm) REVERT: E 31 LYS cc_start: 0.7899 (mmpt) cc_final: 0.7374 (tttm) REVERT: E 151 ASP cc_start: 0.8840 (m-30) cc_final: 0.8489 (t0) REVERT: F 196 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.6070 (tmt170) REVERT: F 219 MET cc_start: 0.6976 (tpt) cc_final: 0.6523 (tpt) REVERT: F 270 ASP cc_start: 0.8333 (m-30) cc_final: 0.7591 (t70) REVERT: F 349 ILE cc_start: 0.9006 (mm) cc_final: 0.8662 (mt) REVERT: F 364 MET cc_start: 0.6864 (tmm) cc_final: 0.6612 (tmm) outliers start: 34 outliers final: 32 residues processed: 349 average time/residue: 0.7253 time to fit residues: 395.3447 Evaluate side-chains 351 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 887 ASP Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 271 PHE Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 111 PHE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 192 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.122600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110435 restraints weight = 130711.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113983 restraints weight = 56661.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115974 restraints weight = 26955.626| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 20966 Z= 0.235 Angle : 0.850 80.630 28742 Z= 0.364 Chirality : 0.079 1.778 3062 Planarity : 0.005 0.060 3661 Dihedral : 8.124 179.825 2816 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 1.68 % Allowed : 17.85 % Favored : 80.47 % 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: -3.13 (0.16), residues: 2490 helix: -1.15 (0.15), residues: 1077 sheet: -4.35 (0.46), residues: 79 loop : -2.82 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 382 HIS 0.011 0.001 HIS C 247 PHE 0.025 0.002 PHE D 111 TYR 0.015 0.001 TYR F 295 ARG 0.009 0.000 ARG E 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8949.71 seconds wall clock time: 159 minutes 2.05 seconds (9542.05 seconds total)