Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/05_2023/6f0k_4165_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/05_2023/6f0k_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_4165/05_2023/6f0k_4165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/05_2023/6f0k_4165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/05_2023/6f0k_4165_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f0k_4165/05_2023/6f0k_4165_trim_updated.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 19.35, per 1000 atoms: 0.49 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: 36.92 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: 2.36 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: 14.79 Time building geometry restraints manager: 38.17 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: 16161 35.93 - 71.86: 102 71.86 - 107.80: 22 107.80 - 143.73: 0 143.73 - 179.66: 2 Dihedral angle restraints: 16287 sinusoidal: 7241 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 16284 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: 1.360 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: 0.670 Extract box with map and model: 9.300 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 143.910 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.420 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.836 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 outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.8219 time to fit residues: 750.0712 Evaluate side-chains 370 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0529 ------------------------------------------------------------------------------- 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: 4.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: