Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 17:46:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1j_22624/05_2023/7k1j_22624.pdb" } resolution = 3.9 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= 0.003 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 224 5.16 5 C 24160 2.51 5 N 6464 2.21 5 O 7120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1265": "OE1" <-> "OE2" Residue "A TYR 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A ARG 1460": "NH1" <-> "NH2" Residue "A GLU 1708": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A GLU 1775": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A GLU 1958": "OE1" <-> "OE2" Residue "A ARG 1987": "NH1" <-> "NH2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A GLU 2087": "OE1" <-> "OE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2243": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A GLU 2974": "OE1" <-> "OE2" Residue "A GLU 3007": "OE1" <-> "OE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A GLU 3448": "OE1" <-> "OE2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A ARG 3593": "NH1" <-> "NH2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3745": "OE1" <-> "OE2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A GLU 4095": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38040 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 28371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3584, 28371 Classifications: {'peptide': 3584} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 146, 'TRANS': 3436} Chain breaks: 22 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 33, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 248 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3954 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4204 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 20.29, per 1000 atoms: 0.53 Number of scatterers: 38040 At special positions: 0 Unit cell: (135.72, 162.4, 241.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 224 16.00 P 72 15.00 O 7120 8.00 N 6464 7.00 C 24160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.05 Conformation dependent library (CDL) restraints added in 5.7 seconds 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8816 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 11 sheets defined 56.7% alpha, 4.3% beta 34 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 13.98 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 25 through 42 removed outlier: 4.215A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 removed outlier: 3.790A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.674A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.578A pdb=" N ASP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.722A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.553A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.554A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 4.336A pdb=" N ASN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.829A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.372A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 4.059A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.080A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 4.130A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 removed outlier: 3.963A pdb=" N ASN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 removed outlier: 4.097A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.825A pdb=" N ILE A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.845A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 642 through 645 removed outlier: 3.592A pdb=" N TRP A 645 " --> pdb=" O PHE A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 646 through 660 Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.882A pdb=" N LEU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.035A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.812A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 removed outlier: 3.927A pdb=" N LYS A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 836 Processing helix chain 'A' and resid 847 through 863 removed outlier: 3.853A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.735A pdb=" N LEU A 870 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 923 through 945 removed outlier: 3.542A pdb=" N VAL A 928 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 974 Proline residue: A 967 - end of helix removed outlier: 4.033A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 984 through 996 removed outlier: 3.556A pdb=" N ILE A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 removed outlier: 3.631A pdb=" N PHE A1001 " --> pdb=" O ASN A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1018 removed outlier: 3.841A pdb=" N VAL A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A1008 " --> pdb=" O GLN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1043 removed outlier: 3.962A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A1043 " --> pdb=" O TRP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1067 Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.934A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1114 removed outlier: 3.670A pdb=" N LEU A1104 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A1105 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1122 removed outlier: 3.840A pdb=" N LEU A1121 " --> pdb=" O GLU A1118 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A1122 " --> pdb=" O LYS A1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1118 through 1122' Processing helix chain 'A' and resid 1123 through 1142 removed outlier: 4.129A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 Processing helix chain 'A' and resid 1183 through 1195 removed outlier: 4.570A pdb=" N LYS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1213 removed outlier: 3.735A pdb=" N LEU A1208 " --> pdb=" O PRO A1204 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A1213 " --> pdb=" O LYS A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1251 through 1266 removed outlier: 3.821A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1273 removed outlier: 4.328A pdb=" N PHE A1270 " --> pdb=" O CYS A1266 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A1272 " --> pdb=" O ASN A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1283 removed outlier: 3.648A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1299 removed outlier: 3.667A pdb=" N ALA A1295 " --> pdb=" O LEU A1291 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1335 removed outlier: 3.663A pdb=" N TYR A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1350 removed outlier: 4.022A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1376 removed outlier: 4.490A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1405 Proline residue: A1396 - end of helix removed outlier: 4.260A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET A1403 " --> pdb=" O CYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1432 removed outlier: 3.708A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1461 removed outlier: 4.095A pdb=" N VAL A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1490 Processing helix chain 'A' and resid 1505 through 1519 removed outlier: 3.723A pdb=" N LEU A1515 " --> pdb=" O ALA A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1556 through 1563 removed outlier: 3.710A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1574 removed outlier: 3.942A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1584 Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.711A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1624 removed outlier: 3.690A pdb=" N GLN A1624 " --> pdb=" O THR A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1629 removed outlier: 3.514A pdb=" N LYS A1628 " --> pdb=" O HIS A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1656 removed outlier: 3.594A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 4.126A pdb=" N ASP A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1689 through 1694 Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.656A pdb=" N PHE A1722 " --> pdb=" O ILE A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1753 Processing helix chain 'A' and resid 1757 through 1767 removed outlier: 3.999A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.910A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.867A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 3.943A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1837 through 1852 removed outlier: 4.201A pdb=" N VAL A1844 " --> pdb=" O PHE A1840 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 3.789A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1911 through 1922 removed outlier: 3.832A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1953 Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.887A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.674A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2037 through 2046 removed outlier: 4.375A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A2044 " --> pdb=" O MET A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2134 removed outlier: 3.761A pdb=" N GLY A2134 " --> pdb=" O HIS A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.795A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A2153 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2161 removed outlier: 3.996A pdb=" N ALA A2161 " --> pdb=" O ARG A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 removed outlier: 4.155A pdb=" N LEU A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2196 removed outlier: 3.722A pdb=" N VAL A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 3.741A pdb=" N VAL A2210 " --> pdb=" O PRO A2206 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 removed outlier: 3.555A pdb=" N PHE A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A2232 " --> pdb=" O ARG A2228 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.880A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2308 removed outlier: 3.880A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.009A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A2317 " --> pdb=" O LYS A2313 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2356 removed outlier: 4.838A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 Processing helix chain 'A' and resid 2375 through 2377 No H-bonds generated for 'chain 'A' and resid 2375 through 2377' Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2402 removed outlier: 4.307A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.510A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 removed outlier: 3.766A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A2439 " --> pdb=" O CYS A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.902A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2483 removed outlier: 3.620A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A2477 " --> pdb=" O MET A2473 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2509 removed outlier: 4.543A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A2506 " --> pdb=" O ALA A2502 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A2507 " --> pdb=" O LYS A2503 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2526 removed outlier: 3.675A pdb=" N ILE A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2542 Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.453A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2799 removed outlier: 4.099A pdb=" N THR A2792 " --> pdb=" O SER A2788 " (cutoff:3.500A) Proline residue: A2793 - end of helix removed outlier: 4.263A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.665A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.671A pdb=" N ASN A2830 " --> pdb=" O LEU A2826 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2862 removed outlier: 4.322A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2881 removed outlier: 3.787A pdb=" N SER A2877 " --> pdb=" O PRO A2873 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.902A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A2891 " --> pdb=" O PRO A2887 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2931 removed outlier: 4.818A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2941 removed outlier: 3.634A pdb=" N LEU A2939 " --> pdb=" O GLU A2935 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A2940 " --> pdb=" O TYR A2936 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2958 Processing helix chain 'A' and resid 2969 through 2977 removed outlier: 3.807A pdb=" N ASP A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3004 Processing helix chain 'A' and resid 3008 through 3017 removed outlier: 3.857A pdb=" N GLU A3012 " --> pdb=" O TRP A3008 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3039 removed outlier: 3.567A pdb=" N GLU A3038 " --> pdb=" O PRO A3034 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A3039 " --> pdb=" O PHE A3035 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3034 through 3039' Processing helix chain 'A' and resid 3040 through 3053 Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.847A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3077 through 3082 removed outlier: 3.636A pdb=" N TYR A3082 " --> pdb=" O LEU A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3092 Processing helix chain 'A' and resid 3097 through 3117 Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3146 Processing helix chain 'A' and resid 3154 through 3165 Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.894A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3228 through 3248 removed outlier: 3.798A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) Processing helix chain 'A' and resid 3252 through 3263 removed outlier: 3.812A pdb=" N LEU A3258 " --> pdb=" O LEU A3254 " (cutoff:3.500A) Processing helix chain 'A' and resid 3264 through 3268 removed outlier: 3.955A pdb=" N LYS A3267 " --> pdb=" O LYS A3264 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A3268 " --> pdb=" O GLU A3265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3264 through 3268' Processing helix chain 'A' and resid 3269 through 3288 removed outlier: 3.846A pdb=" N LEU A3273 " --> pdb=" O ARG A3269 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3302 removed outlier: 3.746A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3304 through 3308 Processing helix chain 'A' and resid 3319 through 3342 removed outlier: 3.687A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3362 removed outlier: 3.905A pdb=" N LEU A3362 " --> pdb=" O ARG A3358 " (cutoff:3.500A) Processing helix chain 'A' and resid 3371 through 3389 removed outlier: 4.243A pdb=" N ALA A3375 " --> pdb=" O GLU A3371 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3425 removed outlier: 3.776A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 3.998A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) Processing helix chain 'A' and resid 3467 through 3475 removed outlier: 4.404A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 3.627A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3530 through 3535 removed outlier: 3.528A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3530 through 3535' Processing helix chain 'A' and resid 3549 through 3562 removed outlier: 3.852A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3581 through 3593 removed outlier: 4.312A pdb=" N LYS A3586 " --> pdb=" O GLU A3582 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A3587 " --> pdb=" O LEU A3583 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP A3588 " --> pdb=" O LEU A3584 " (cutoff:3.500A) Processing helix chain 'A' and resid 3609 through 3615 removed outlier: 3.681A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3627 Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3641 through 3650 removed outlier: 4.120A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3651 through 3654 removed outlier: 4.147A pdb=" N MET A3654 " --> pdb=" O LEU A3651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3651 through 3654' Processing helix chain 'A' and resid 3660 through 3671 Processing helix chain 'A' and resid 3680 through 3684 removed outlier: 3.903A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3775 removed outlier: 3.889A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.890A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3823 through 3830 Processing helix chain 'A' and resid 3834 through 3847 Processing helix chain 'A' and resid 3854 through 3859 removed outlier: 3.922A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 4.119A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3892 removed outlier: 4.054A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A3892 " --> pdb=" O VAL A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3915 removed outlier: 4.192A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A3904 " --> pdb=" O LEU A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3948 through 3953 removed outlier: 3.972A pdb=" N PHE A3952 " --> pdb=" O SER A3948 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3948 through 3953' Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3996 through 4006 removed outlier: 3.527A pdb=" N VAL A4006 " --> pdb=" O MET A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4023 removed outlier: 4.269A pdb=" N LYS A4023 " --> pdb=" O LYS A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4042 through 4050 Processing helix chain 'A' and resid 4057 through 4066 Processing helix chain 'A' and resid 4074 through 4083 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.591A pdb=" N THR A4112 " --> pdb=" O MET A4108 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.959A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 143 through 155 removed outlier: 4.473A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 removed outlier: 3.602A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 377 through 392 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.873A pdb=" N LEU B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 4.094A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 87 through 96 removed outlier: 3.790A pdb=" N LEU C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 227 through 232 removed outlier: 4.143A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 232' Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.759A pdb=" N PHE C 355 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 356 " --> pdb=" O ARG C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.901A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 517 removed outlier: 4.115A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.902A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.699A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3810 through 3811 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.664A pdb=" N ASP B 36 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 42 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ARG B 35 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 164 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER B 37 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE B 166 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 39 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 168 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 41 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 262 removed outlier: 9.044A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 299 through 303 removed outlier: 3.704A pdb=" N PHE B 303 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.870A pdb=" N ARG B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.565A pdb=" N LEU C 58 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 247 through 251 removed outlier: 5.171A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 344 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C 394 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL C 342 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA C 396 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 464 through 466 1602 hydrogen bonds defined for protein. 4716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 27.81 Time building geometry restraints manager: 17.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9310 1.33 - 1.45: 8523 1.45 - 1.58: 20625 1.58 - 1.70: 142 1.70 - 1.82: 351 Bond restraints: 38951 Sorted by residual: bond pdb=" C MET A3959 " pdb=" N PRO A3960 " ideal model delta sigma weight residual 1.337 1.293 0.044 1.24e-02 6.50e+03 1.24e+01 bond pdb=" C MET A2443 " pdb=" N PRO A2444 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 9.97e+00 bond pdb=" N ASP A2121 " pdb=" CA ASP A2121 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.82e+00 bond pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.24e+00 bond pdb=" N SER A2124 " pdb=" CA SER A2124 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.57e+00 ... (remaining 38946 not shown) Histogram of bond angle deviations from ideal: 95.14 - 103.66: 725 103.66 - 112.17: 18902 112.17 - 120.69: 21183 120.69 - 129.21: 11848 129.21 - 137.73: 300 Bond angle restraints: 52958 Sorted by residual: angle pdb=" C LEU A 634 " pdb=" N PRO A 635 " pdb=" CA PRO A 635 " ideal model delta sigma weight residual 119.84 137.73 -17.89 1.25e+00 6.40e-01 2.05e+02 angle pdb=" O ARG B 244 " pdb=" C ARG B 244 " pdb=" N LYS B 245 " ideal model delta sigma weight residual 121.79 129.62 -7.83 9.80e-01 1.04e+00 6.38e+01 angle pdb=" CA PHE A1923 " pdb=" CB PHE A1923 " pdb=" CG PHE A1923 " ideal model delta sigma weight residual 113.80 121.45 -7.65 1.00e+00 1.00e+00 5.85e+01 angle pdb=" C SER A1554 " pdb=" N HIS A1555 " pdb=" CA HIS A1555 " ideal model delta sigma weight residual 121.54 107.53 14.01 1.91e+00 2.74e-01 5.38e+01 angle pdb=" C ARG B 244 " pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.03e+01 ... (remaining 52953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19823 17.91 - 35.81: 2813 35.81 - 53.72: 695 53.72 - 71.62: 134 71.62 - 89.53: 34 Dihedral angle restraints: 23499 sinusoidal: 9976 harmonic: 13523 Sorted by residual: dihedral pdb=" CA MET C 427 " pdb=" C MET C 427 " pdb=" N GLU C 428 " pdb=" CA GLU C 428 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN A3772 " pdb=" C ASN A3772 " pdb=" N GLY A3773 " pdb=" CA GLY A3773 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA MET A 333 " pdb=" C MET A 333 " pdb=" N HIS A 334 " pdb=" CA HIS A 334 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 23496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5078 0.088 - 0.175: 869 0.175 - 0.263: 91 0.263 - 0.351: 4 0.351 - 0.439: 1 Chirality restraints: 6043 Sorted by residual: chirality pdb=" CB ILE A 125 " pdb=" CA ILE A 125 " pdb=" CG1 ILE A 125 " pdb=" CG2 ILE A 125 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB VAL A1054 " pdb=" CA VAL A1054 " pdb=" CG1 VAL A1054 " pdb=" CG2 VAL A1054 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 100 " pdb=" CA ILE A 100 " pdb=" CG1 ILE A 100 " pdb=" CG2 ILE A 100 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 6040 not shown) Planarity restraints: 6469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1553 " -0.039 2.00e-02 2.50e+03 8.09e-02 6.54e+01 pdb=" C PHE A1553 " 0.140 2.00e-02 2.50e+03 pdb=" O PHE A1553 " -0.055 2.00e-02 2.50e+03 pdb=" N SER A1554 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 524 " 0.027 2.00e-02 2.50e+03 5.41e-02 2.92e+01 pdb=" C TYR A 524 " -0.093 2.00e-02 2.50e+03 pdb=" O TYR A 524 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 525 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 976 " -0.024 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C VAL A 976 " 0.087 2.00e-02 2.50e+03 pdb=" O VAL A 976 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP A 977 " -0.029 2.00e-02 2.50e+03 ... (remaining 6466 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 603 2.63 - 3.20: 32796 3.20 - 3.77: 57944 3.77 - 4.33: 73901 4.33 - 4.90: 119431 Nonbonded interactions: 284675 Sorted by model distance: nonbonded pdb=" O ASN A2977 " pdb=" O LYS A2978 " model vdw 2.066 3.040 nonbonded pdb=" O LYS B 245 " pdb=" CG1 VAL B 246 " model vdw 2.121 3.460 nonbonded pdb=" O LEU A2194 " pdb=" OG1 THR A2197 " model vdw 2.217 2.440 nonbonded pdb=" O ILE A 488 " pdb=" OG SER A 492 " model vdw 2.231 2.440 nonbonded pdb=" O TRP A2994 " pdb=" OG SER A2998 " model vdw 2.237 2.440 ... (remaining 284670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and resid 4 through 24) selection = chain 'F' } 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 13.770 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 118.080 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.190 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.010 0.117 38951 Z= 0.618 Angle : 1.241 20.530 52958 Z= 0.660 Chirality : 0.066 0.439 6043 Planarity : 0.009 0.099 6469 Dihedral : 17.625 89.528 14683 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.50 % Favored : 84.98 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % 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: -5.24 (0.09), residues: 4546 helix: -3.03 (0.07), residues: 2493 sheet: -1.96 (0.35), residues: 195 loop : -4.22 (0.12), residues: 1858 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 580 time to evaluate : 4.560 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 outliers start: 44 outliers final: 19 residues processed: 617 average time/residue: 0.6003 time to fit residues: 596.6722 Evaluate side-chains 420 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 401 time to evaluate : 4.545 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3405 time to fit residues: 19.0292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 0.8980 chunk 352 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 188 optimal weight: 0.2980 chunk 364 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 422 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 415 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 720 GLN A 833 HIS A1126 GLN A1142 HIS ** A1205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN A1737 ASN A1830 HIS A1859 ASN A1866 GLN A1941 HIS A2042 GLN A2105 HIS ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2348 GLN A2518 GLN A2523 ASN ** A2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2795 GLN A2841 ASN A2885 GLN A3104 GLN A3327 ASN A3383 GLN A3470 GLN A3501 HIS ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3573 ASN A3697 ASN A3924 HIS A3926 ASN A3927 ASN A3966 GLN A4087 HIS B 98 ASN B 152 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 486 HIS ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN C 45 GLN C 75 GLN C 76 ASN C 103 GLN C 119 GLN C 131 HIS C 246 HIS ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 38951 Z= 0.275 Angle : 0.768 12.055 52958 Z= 0.399 Chirality : 0.045 0.235 6043 Planarity : 0.006 0.086 6469 Dihedral : 13.881 84.667 5652 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.71 % Favored : 87.20 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.93 (0.11), residues: 4546 helix: -1.72 (0.09), residues: 2511 sheet: -1.65 (0.36), residues: 195 loop : -4.00 (0.12), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 460 time to evaluate : 4.768 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 outliers start: 108 outliers final: 52 residues processed: 541 average time/residue: 0.5081 time to fit residues: 461.0919 Evaluate side-chains 444 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 392 time to evaluate : 4.542 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3735 time to fit residues: 43.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 4.9990 chunk 131 optimal weight: 0.1980 chunk 351 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 423 optimal weight: 20.0000 chunk 456 optimal weight: 2.9990 chunk 376 optimal weight: 0.7980 chunk 419 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 339 optimal weight: 0.0980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 409 GLN A 442 GLN ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2518 GLN A2543 ASN A3278 GLN ** A3516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3926 ASN B 264 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 76 ASN C 119 GLN C 414 HIS ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 38951 Z= 0.176 Angle : 0.663 10.629 52958 Z= 0.342 Chirality : 0.042 0.243 6043 Planarity : 0.005 0.080 6469 Dihedral : 13.457 83.672 5652 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.94 % Favored : 87.97 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.12 (0.12), residues: 4546 helix: -0.99 (0.10), residues: 2530 sheet: -1.33 (0.38), residues: 195 loop : -3.78 (0.13), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 474 time to evaluate : 4.654 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 outliers start: 89 outliers final: 33 residues processed: 541 average time/residue: 0.5027 time to fit residues: 459.1465 Evaluate side-chains 447 residues out of total 4126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 414 time to evaluate : 5.041 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3581 time to fit residues: 27.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2111 > 50: distance: 27 - 31: 12.113 distance: 31 - 32: 7.364 distance: 32 - 33: 8.634 distance: 32 - 35: 7.393 distance: 33 - 34: 20.382 distance: 33 - 42: 4.090 distance: 35 - 36: 15.014 distance: 36 - 37: 12.333 distance: 36 - 38: 5.793 distance: 37 - 39: 19.360 distance: 38 - 40: 10.421 distance: 39 - 41: 20.500 distance: 40 - 41: 17.090 distance: 42 - 43: 32.302 distance: 43 - 44: 14.077 distance: 43 - 46: 11.102 distance: 44 - 45: 27.782 distance: 44 - 49: 12.431 distance: 46 - 47: 10.264 distance: 46 - 48: 20.276 distance: 49 - 50: 13.852 distance: 50 - 51: 17.725 distance: 50 - 53: 13.761 distance: 51 - 52: 33.637 distance: 51 - 55: 14.010 distance: 53 - 54: 27.443 distance: 55 - 56: 16.068 distance: 56 - 57: 12.232 distance: 56 - 59: 24.542 distance: 57 - 58: 23.638 distance: 57 - 65: 30.895 distance: 59 - 60: 27.235 distance: 60 - 61: 30.852 distance: 60 - 62: 24.357 distance: 61 - 63: 10.159 distance: 62 - 64: 11.810 distance: 63 - 64: 36.951 distance: 65 - 66: 28.146 distance: 65 - 71: 29.816 distance: 66 - 67: 19.364 distance: 66 - 69: 34.032 distance: 67 - 68: 14.680 distance: 67 - 72: 21.396 distance: 69 - 70: 13.723 distance: 70 - 71: 23.073 distance: 72 - 73: 21.425 distance: 73 - 74: 34.988 distance: 73 - 76: 20.156 distance: 74 - 75: 13.893 distance: 74 - 78: 23.197 distance: 76 - 77: 18.237 distance: 78 - 79: 16.091 distance: 79 - 80: 22.541 distance: 79 - 82: 16.023 distance: 80 - 81: 13.779 distance: 80 - 85: 15.416 distance: 81 - 109: 34.764 distance: 82 - 83: 11.217 distance: 82 - 84: 26.687 distance: 85 - 86: 17.761 distance: 86 - 87: 26.720 distance: 86 - 89: 34.313 distance: 87 - 88: 21.142 distance: 88 - 115: 26.437 distance: 89 - 90: 27.748 distance: 89 - 91: 37.130 distance: 92 - 93: 6.880 distance: 93 - 94: 5.207 distance: 93 - 96: 14.861 distance: 94 - 95: 14.882 distance: 94 - 98: 25.731 distance: 95 - 121: 20.902 distance: 96 - 97: 39.742 distance: 98 - 99: 4.363 distance: 99 - 100: 15.759 distance: 99 - 102: 19.979 distance: 100 - 101: 23.643 distance: 100 - 109: 6.263 distance: 101 - 128: 22.307 distance: 102 - 103: 21.146 distance: 103 - 104: 8.870 distance: 104 - 105: 6.001 distance: 105 - 106: 9.984 distance: 106 - 107: 6.479 distance: 106 - 108: 19.663