Starting phenix.real_space_refine on Mon Mar 25 22:40:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/03_2024/6uqk_20849.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.917 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 Zn 4 6.06 5 S 56 5.16 5 C 32635 2.51 5 N 9748 2.21 5 O 9124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2128": "NH1" <-> "NH2" Residue "A ARG 2304": "NH1" <-> "NH2" Residue "A PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2524": "NH1" <-> "NH2" Residue "A TYR 2568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B GLU 1000": "OE1" <-> "OE2" Residue "B PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2128": "NH1" <-> "NH2" Residue "B ARG 2304": "NH1" <-> "NH2" Residue "B PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2524": "NH1" <-> "NH2" Residue "B TYR 2568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C GLU 1000": "OE1" <-> "OE2" Residue "C PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2128": "NH1" <-> "NH2" Residue "C ARG 2304": "NH1" <-> "NH2" Residue "C PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2524": "NH1" <-> "NH2" Residue "C TYR 2568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D GLU 1000": "OE1" <-> "OE2" Residue "D PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2128": "NH1" <-> "NH2" Residue "D ARG 2304": "NH1" <-> "NH2" Residue "D PHE 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2524": "NH1" <-> "NH2" Residue "D TYR 2568": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2054, 12890 Classifications: {'peptide': 2054} Incomplete info: {'backbone_only': 1, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 57, 'TRANS': 1996} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3720 Unresolved non-hydrogen angles: 4703 Unresolved non-hydrogen dihedrals: 2822 Unresolved non-hydrogen chiralities: 453 Planarities with less than four sites: {'GLN:plan1': 69, 'UNK:plan-1': 46, 'ASP:plan': 91, 'TYR:plan': 7, 'ASN:plan1': 69, 'HIS:plan': 16, 'PHE:plan': 16, 'GLU:plan': 129, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1744 Chain: "B" Number of atoms: 12891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2054, 12891 Classifications: {'peptide': 2054} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 57, 'TRANS': 1996} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3719 Unresolved non-hydrogen angles: 4701 Unresolved non-hydrogen dihedrals: 2822 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLN:plan1': 69, 'UNK:plan-1': 46, 'ASP:plan': 91, 'TYR:plan': 7, 'ASN:plan1': 69, 'HIS:plan': 16, 'PHE:plan': 16, 'GLU:plan': 129, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1743 Chain: "C" Number of atoms: 12891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2054, 12891 Classifications: {'peptide': 2054} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 57, 'TRANS': 1996} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3719 Unresolved non-hydrogen angles: 4701 Unresolved non-hydrogen dihedrals: 2822 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLN:plan1': 69, 'UNK:plan-1': 46, 'ASP:plan': 91, 'TYR:plan': 7, 'ASN:plan1': 69, 'HIS:plan': 16, 'PHE:plan': 16, 'GLU:plan': 129, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1743 Chain: "D" Number of atoms: 12891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2054, 12891 Classifications: {'peptide': 2054} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 57, 'TRANS': 1996} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3719 Unresolved non-hydrogen angles: 4701 Unresolved non-hydrogen dihedrals: 2822 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLN:plan1': 69, 'UNK:plan-1': 46, 'ASP:plan': 91, 'TYR:plan': 7, 'ASN:plan1': 69, 'HIS:plan': 16, 'PHE:plan': 16, 'GLU:plan': 129, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1743 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12288 SG CYS A2538 107.457 99.162 107.351 1.00 98.57 S ATOM 12313 SG CYS A2541 111.259 100.418 105.558 1.00101.34 S ATOM 25179 SG CYS B2538 99.204 126.902 107.477 1.00 98.28 S ATOM 25204 SG CYS B2541 100.457 123.103 105.676 1.00100.98 S ATOM 38070 SG CYS C2538 127.071 135.180 107.406 1.00 98.70 S ATOM 38095 SG CYS C2541 123.268 133.928 105.611 1.00101.66 S ATOM 50961 SG CYS D2538 135.206 107.587 107.485 1.00 97.38 S ATOM 50986 SG CYS D2541 133.958 111.385 105.678 1.00101.74 S Time building chain proxies: 28.43, per 1000 atoms: 0.55 Number of scatterers: 51567 At special positions: 0 Unit cell: (235.683, 235.683, 195.779, 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) Zn 4 29.99 S 56 16.00 O 9124 8.00 N 9748 7.00 C 32635 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: 20.67 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4000 " pdb="ZN ZN A4000 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A4000 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A4000 " - pdb=" SG CYS A2541 " pdb="ZN ZN A4000 " - pdb=" SG CYS A2538 " pdb=" ZN B4000 " pdb="ZN ZN B4000 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B4000 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B4000 " - pdb=" SG CYS B2541 " pdb="ZN ZN B4000 " - pdb=" SG CYS B2538 " pdb=" ZN C4000 " pdb="ZN ZN C4000 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C4000 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C4000 " - pdb=" SG CYS C2541 " pdb="ZN ZN C4000 " - pdb=" SG CYS C2538 " pdb=" ZN D4000 " pdb="ZN ZN D4000 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D4000 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D4000 " - pdb=" SG CYS D2541 " pdb="ZN ZN D4000 " - pdb=" SG CYS D2538 " Number of angles added : 8 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15718 Finding SS restraints... Secondary structure from input PDB file: 384 helices and 40 sheets defined 64.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.41 Creating SS restraints... Processing helix chain 'A' and resid 51 through 54 removed outlier: 3.542A pdb=" N ASP A 54 " --> pdb=" O LYS A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.694A pdb=" N LYS A 69 " --> pdb=" O TYR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.589A pdb=" N SER A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.823A pdb=" N SER A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.820A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 484 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 546 through 563 Processing helix chain 'A' and resid 567 through 577 removed outlier: 4.082A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.733A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.854A pdb=" N LEU A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.556A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.718A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 739 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.557A pdb=" N ILE A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.914A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 760 " --> pdb=" O GLY A 756 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 removed outlier: 3.824A pdb=" N ARG A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 3.829A pdb=" N ASP A 816 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.668A pdb=" N PHE A 861 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 890 Processing helix chain 'A' and resid 962 through 1001 Processing helix chain 'A' and resid 1026 through 1035 Processing helix chain 'A' and resid 1051 through 1064 removed outlier: 3.673A pdb=" N PHE A1055 " --> pdb=" O GLY A1051 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1058 " --> pdb=" O MET A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1082 removed outlier: 3.863A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'A' and resid 1100 through 1127 Processing helix chain 'A' and resid 1171 through 1181 Processing helix chain 'A' and resid 1187 through 1200 Processing helix chain 'A' and resid 1202 through 1211 removed outlier: 3.824A pdb=" N MET A1206 " --> pdb=" O ALA A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1236 Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 3.841A pdb=" N PHE A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1268 removed outlier: 3.707A pdb=" N ALA A1261 " --> pdb=" O GLY A1257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1276 Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.532A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A1294 " --> pdb=" O LEU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1308 removed outlier: 3.768A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 4.319A pdb=" N ASP A1319 " --> pdb=" O LYS A1315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A1320 " --> pdb=" O LYS A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 4.042A pdb=" N LEU A1342 " --> pdb=" O ASP A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1376 removed outlier: 3.543A pdb=" N ALA A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1391 removed outlier: 3.526A pdb=" N GLU A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1409 through 1416 removed outlier: 4.139A pdb=" N TYR A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1477 Processing helix chain 'A' and resid 1588 through 1623 Proline residue: A1608 - end of helix Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1635 through 1639 Processing helix chain 'A' and resid 1642 through 1654 Processing helix chain 'A' and resid 1658 through 1673 removed outlier: 3.600A pdb=" N CYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1718 through 1731 Processing helix chain 'A' and resid 1732 through 1743 removed outlier: 3.541A pdb=" N LEU A1736 " --> pdb=" O GLY A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1761 Processing helix chain 'A' and resid 1765 through 1778 removed outlier: 3.565A pdb=" N SER A1778 " --> pdb=" O ASN A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1803 Processing helix chain 'A' and resid 1864 through 1881 Proline residue: A1872 - end of helix removed outlier: 3.645A pdb=" N CYS A1881 " --> pdb=" O LEU A1877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1894 Processing helix chain 'A' and resid 1902 through 1916 Processing helix chain 'A' and resid 1922 through 1927 removed outlier: 3.521A pdb=" N LEU A1927 " --> pdb=" O GLY A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1948 removed outlier: 3.611A pdb=" N VAL A1937 " --> pdb=" O ASN A1933 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS A1948 " --> pdb=" O LEU A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1959 Processing helix chain 'A' and resid 1968 through 1976 Processing helix chain 'A' and resid 1981 through 1984 removed outlier: 4.119A pdb=" N TYR A1984 " --> pdb=" O LEU A1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1981 through 1984' Processing helix chain 'A' and resid 1985 through 2004 removed outlier: 4.043A pdb=" N VAL A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2020 Processing helix chain 'A' and resid 2021 through 2036 removed outlier: 4.168A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2061 removed outlier: 3.850A pdb=" N VAL A2049 " --> pdb=" O SER A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2120 Processing helix chain 'A' and resid 2148 through 2158 removed outlier: 3.788A pdb=" N LYS A2152 " --> pdb=" O THR A2148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A2157 " --> pdb=" O HIS A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2190 removed outlier: 4.182A pdb=" N PHE A2172 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A2173 " --> pdb=" O SER A2169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN A2174 " --> pdb=" O ASP A2170 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2200 removed outlier: 4.261A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2220 removed outlier: 4.400A pdb=" N TRP A2204 " --> pdb=" O ARG A2200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A2205 " --> pdb=" O MET A2201 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER A2206 " --> pdb=" O THR A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2244 Processing helix chain 'A' and resid 2264 through 2275 Processing helix chain 'A' and resid 2277 through 2304 removed outlier: 3.562A pdb=" N ARG A2304 " --> pdb=" O PHE A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2317 removed outlier: 3.779A pdb=" N MET A2316 " --> pdb=" O ALA A2313 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A2317 " --> pdb=" O MET A2314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2313 through 2317' Processing helix chain 'A' and resid 2319 through 2336 removed outlier: 3.880A pdb=" N HIS A2323 " --> pdb=" O GLU A2319 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 2340 through 2345 removed outlier: 3.835A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2347 through 2352 Processing helix chain 'A' and resid 2355 through 2364 removed outlier: 3.613A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2391 Processing helix chain 'A' and resid 2392 through 2395 removed outlier: 3.966A pdb=" N PHE A2395 " --> pdb=" O LYS A2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2392 through 2395' Processing helix chain 'A' and resid 2458 through 2471 removed outlier: 3.639A pdb=" N ILE A2462 " --> pdb=" O LEU A2458 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2505 Processing helix chain 'A' and resid 2509 through 2536 Processing helix chain 'A' and resid 2554 through 2559 Processing helix chain 'A' and resid 2564 through 2578 removed outlier: 4.014A pdb=" N TYR A2568 " --> pdb=" O ASN A2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A2569 " --> pdb=" O MET A2565 " (cutoff:3.500A) Processing helix chain 'A' and resid 2586 through 2596 removed outlier: 3.694A pdb=" N ASN A2596 " --> pdb=" O GLN A2592 " (cutoff:3.500A) Processing helix chain 'A' and resid 2623 through 2642 Processing helix chain 'B' and resid 51 through 54 removed outlier: 3.543A pdb=" N ASP B 54 " --> pdb=" O LYS B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.694A pdb=" N LYS B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.590A pdb=" N SER B 160 " --> pdb=" O ASN B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 362 through 365 removed outlier: 3.823A pdb=" N SER B 365 " --> pdb=" O ASP B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 365' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.821A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 484 Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 546 through 563 Processing helix chain 'B' and resid 567 through 577 removed outlier: 4.082A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 590 through 599 removed outlier: 3.733A pdb=" N THR B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 599 " --> pdb=" O ILE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.853A pdb=" N LEU B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.557A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 removed outlier: 3.718A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 634 " --> pdb=" O PHE B 630 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 739 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.556A pdb=" N ILE B 751 " --> pdb=" O ALA B 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 752 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 764 removed outlier: 3.915A pdb=" N LEU B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 761 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B 764 " --> pdb=" O ILE B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 786 removed outlier: 3.824A pdb=" N ARG B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 819 removed outlier: 3.830A pdb=" N ASP B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 853 through 874 removed outlier: 3.668A pdb=" N PHE B 861 " --> pdb=" O ASN B 857 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 862 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 890 Processing helix chain 'B' and resid 962 through 1001 Processing helix chain 'B' and resid 1026 through 1035 Processing helix chain 'B' and resid 1051 through 1064 removed outlier: 3.673A pdb=" N PHE B1055 " --> pdb=" O GLY B1051 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1082 removed outlier: 3.863A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1095 Processing helix chain 'B' and resid 1100 through 1127 Processing helix chain 'B' and resid 1171 through 1181 Processing helix chain 'B' and resid 1187 through 1200 Processing helix chain 'B' and resid 1202 through 1211 removed outlier: 3.824A pdb=" N MET B1206 " --> pdb=" O ALA B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1236 Processing helix chain 'B' and resid 1239 through 1249 Processing helix chain 'B' and resid 1249 through 1254 removed outlier: 3.842A pdb=" N PHE B1253 " --> pdb=" O HIS B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1268 removed outlier: 3.707A pdb=" N ALA B1261 " --> pdb=" O GLY B1257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1271 through 1276 Processing helix chain 'B' and resid 1279 through 1294 removed outlier: 3.532A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B1294 " --> pdb=" O LEU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1308 removed outlier: 3.769A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1328 removed outlier: 4.320A pdb=" N ASP B1319 " --> pdb=" O LYS B1315 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B1320 " --> pdb=" O LYS B1316 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1344 removed outlier: 4.041A pdb=" N LEU B1342 " --> pdb=" O ASP B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1376 removed outlier: 3.544A pdb=" N ALA B1376 " --> pdb=" O LEU B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1391 removed outlier: 3.527A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1401 Processing helix chain 'B' and resid 1409 through 1416 removed outlier: 4.140A pdb=" N TYR B1413 " --> pdb=" O VAL B1409 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1477 Processing helix chain 'B' and resid 1588 through 1623 Proline residue: B1608 - end of helix Processing helix chain 'B' and resid 1624 through 1629 Processing helix chain 'B' and resid 1635 through 1639 Processing helix chain 'B' and resid 1642 through 1654 Processing helix chain 'B' and resid 1658 through 1673 removed outlier: 3.600A pdb=" N CYS B1662 " --> pdb=" O GLU B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1696 removed outlier: 3.885A pdb=" N GLN B1696 " --> pdb=" O GLN B1692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1718 through 1731 Processing helix chain 'B' and resid 1732 through 1743 removed outlier: 3.540A pdb=" N LEU B1736 " --> pdb=" O GLY B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1746 through 1761 Processing helix chain 'B' and resid 1765 through 1778 removed outlier: 3.566A pdb=" N SER B1778 " --> pdb=" O ASN B1774 " (cutoff:3.500A) Processing helix chain 'B' and resid 1781 through 1803 Processing helix chain 'B' and resid 1864 through 1881 Proline residue: B1872 - end of helix removed outlier: 3.645A pdb=" N CYS B1881 " --> pdb=" O LEU B1877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1885 through 1894 Processing helix chain 'B' and resid 1902 through 1916 Processing helix chain 'B' and resid 1922 through 1927 removed outlier: 3.521A pdb=" N LEU B1927 " --> pdb=" O GLY B1923 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1948 removed outlier: 3.610A pdb=" N VAL B1937 " --> pdb=" O ASN B1933 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B1948 " --> pdb=" O LEU B1944 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1959 Processing helix chain 'B' and resid 1968 through 1976 Processing helix chain 'B' and resid 1981 through 1984 removed outlier: 4.119A pdb=" N TYR B1984 " --> pdb=" O LEU B1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1981 through 1984' Processing helix chain 'B' and resid 1985 through 2004 removed outlier: 4.042A pdb=" N VAL B1989 " --> pdb=" O ARG B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2020 Processing helix chain 'B' and resid 2021 through 2036 removed outlier: 4.168A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2061 removed outlier: 3.849A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2120 Processing helix chain 'B' and resid 2148 through 2158 removed outlier: 3.788A pdb=" N LYS B2152 " --> pdb=" O THR B2148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B2157 " --> pdb=" O HIS B2153 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2190 removed outlier: 4.182A pdb=" N PHE B2172 " --> pdb=" O VAL B2168 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP B2173 " --> pdb=" O SER B2169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN B2174 " --> pdb=" O ASP B2170 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2200 removed outlier: 4.261A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2200 through 2220 removed outlier: 4.401A pdb=" N TRP B2204 " --> pdb=" O ARG B2200 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B2205 " --> pdb=" O MET B2201 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B2206 " --> pdb=" O THR B2202 " (cutoff:3.500A) Processing helix chain 'B' and resid 2238 through 2244 Processing helix chain 'B' and resid 2264 through 2275 Processing helix chain 'B' and resid 2277 through 2304 removed outlier: 3.562A pdb=" N ARG B2304 " --> pdb=" O PHE B2300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2317 removed outlier: 3.779A pdb=" N MET B2316 " --> pdb=" O ALA B2313 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B2317 " --> pdb=" O MET B2314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2313 through 2317' Processing helix chain 'B' and resid 2319 through 2336 removed outlier: 3.879A pdb=" N HIS B2323 " --> pdb=" O GLU B2319 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 2340 through 2345 removed outlier: 3.835A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2352 Processing helix chain 'B' and resid 2355 through 2364 removed outlier: 3.612A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2391 Processing helix chain 'B' and resid 2392 through 2395 removed outlier: 3.966A pdb=" N PHE B2395 " --> pdb=" O LYS B2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2392 through 2395' Processing helix chain 'B' and resid 2458 through 2471 removed outlier: 3.638A pdb=" N ILE B2462 " --> pdb=" O LEU B2458 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2505 Processing helix chain 'B' and resid 2509 through 2536 Processing helix chain 'B' and resid 2554 through 2559 Processing helix chain 'B' and resid 2564 through 2578 removed outlier: 4.013A pdb=" N TYR B2568 " --> pdb=" O ASN B2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B2569 " --> pdb=" O MET B2565 " (cutoff:3.500A) Processing helix chain 'B' and resid 2586 through 2596 removed outlier: 3.693A pdb=" N ASN B2596 " --> pdb=" O GLN B2592 " (cutoff:3.500A) Processing helix chain 'B' and resid 2623 through 2642 Processing helix chain 'C' and resid 51 through 54 removed outlier: 3.542A pdb=" N ASP C 54 " --> pdb=" O LYS C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.695A pdb=" N LYS C 69 " --> pdb=" O TYR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 157 through 160 removed outlier: 3.589A pdb=" N SER C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 160' Processing helix chain 'C' and resid 362 through 365 removed outlier: 3.823A pdb=" N SER C 365 " --> pdb=" O ASP C 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 365' Processing helix chain 'C' and resid 435 through 462 removed outlier: 3.820A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 514 through 524 Processing helix chain 'C' and resid 546 through 563 Processing helix chain 'C' and resid 567 through 577 removed outlier: 4.082A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 583 through 585 No H-bonds generated for 'chain 'C' and resid 583 through 585' Processing helix chain 'C' and resid 590 through 599 removed outlier: 3.732A pdb=" N THR C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 609 removed outlier: 3.854A pdb=" N LEU C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 626 removed outlier: 3.557A pdb=" N VAL C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN C 625 " --> pdb=" O LEU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 638 removed outlier: 3.717A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 633 " --> pdb=" O ARG C 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 634 " --> pdb=" O PHE C 630 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS C 638 " --> pdb=" O LEU C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 658 through 662 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 739 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.556A pdb=" N ILE C 751 " --> pdb=" O ALA C 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 752 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 764 removed outlier: 3.915A pdb=" N LEU C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 760 " --> pdb=" O GLY C 756 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 761 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 764 " --> pdb=" O ILE C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 786 removed outlier: 3.824A pdb=" N ARG C 774 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 819 removed outlier: 3.829A pdb=" N ASP C 816 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 817 " --> pdb=" O LYS C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 853 through 874 removed outlier: 3.668A pdb=" N PHE C 861 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 862 " --> pdb=" O LYS C 858 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 890 Processing helix chain 'C' and resid 962 through 1001 Processing helix chain 'C' and resid 1026 through 1035 Processing helix chain 'C' and resid 1051 through 1064 removed outlier: 3.673A pdb=" N PHE C1055 " --> pdb=" O GLY C1051 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C1058 " --> pdb=" O MET C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1082 removed outlier: 3.862A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'C' and resid 1100 through 1127 Processing helix chain 'C' and resid 1171 through 1181 Processing helix chain 'C' and resid 1187 through 1200 Processing helix chain 'C' and resid 1202 through 1211 removed outlier: 3.824A pdb=" N MET C1206 " --> pdb=" O ALA C1202 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1236 Processing helix chain 'C' and resid 1239 through 1249 Processing helix chain 'C' and resid 1249 through 1254 removed outlier: 3.841A pdb=" N PHE C1253 " --> pdb=" O HIS C1249 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1268 removed outlier: 3.707A pdb=" N ALA C1261 " --> pdb=" O GLY C1257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1276 Processing helix chain 'C' and resid 1279 through 1294 removed outlier: 3.532A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C1294 " --> pdb=" O LEU C1290 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1308 removed outlier: 3.768A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1328 removed outlier: 4.319A pdb=" N ASP C1319 " --> pdb=" O LYS C1315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C1320 " --> pdb=" O LYS C1316 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1344 removed outlier: 4.041A pdb=" N LEU C1342 " --> pdb=" O ASP C1338 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1376 removed outlier: 3.544A pdb=" N ALA C1376 " --> pdb=" O LEU C1372 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1391 removed outlier: 3.527A pdb=" N GLU C1384 " --> pdb=" O ASN C1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 1392 through 1401 Processing helix chain 'C' and resid 1409 through 1416 removed outlier: 4.139A pdb=" N TYR C1413 " --> pdb=" O VAL C1409 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1477 Processing helix chain 'C' and resid 1588 through 1623 Proline residue: C1608 - end of helix Processing helix chain 'C' and resid 1624 through 1629 Processing helix chain 'C' and resid 1635 through 1639 Processing helix chain 'C' and resid 1642 through 1654 Processing helix chain 'C' and resid 1658 through 1673 removed outlier: 3.601A pdb=" N CYS C1662 " --> pdb=" O GLU C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1696 removed outlier: 3.886A pdb=" N GLN C1696 " --> pdb=" O GLN C1692 " (cutoff:3.500A) Processing helix chain 'C' and resid 1718 through 1731 Processing helix chain 'C' and resid 1732 through 1743 removed outlier: 3.540A pdb=" N LEU C1736 " --> pdb=" O GLY C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1746 through 1761 Processing helix chain 'C' and resid 1765 through 1778 removed outlier: 3.566A pdb=" N SER C1778 " --> pdb=" O ASN C1774 " (cutoff:3.500A) Processing helix chain 'C' and resid 1781 through 1803 Processing helix chain 'C' and resid 1864 through 1881 Proline residue: C1872 - end of helix removed outlier: 3.645A pdb=" N CYS C1881 " --> pdb=" O LEU C1877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 Processing helix chain 'C' and resid 1922 through 1927 removed outlier: 3.521A pdb=" N LEU C1927 " --> pdb=" O GLY C1923 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1948 removed outlier: 3.610A pdb=" N VAL C1937 " --> pdb=" O ASN C1933 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS C1948 " --> pdb=" O LEU C1944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1959 Processing helix chain 'C' and resid 1968 through 1976 Processing helix chain 'C' and resid 1981 through 1984 removed outlier: 4.119A pdb=" N TYR C1984 " --> pdb=" O LEU C1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1981 through 1984' Processing helix chain 'C' and resid 1985 through 2004 removed outlier: 4.041A pdb=" N VAL C1989 " --> pdb=" O ARG C1985 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2020 Processing helix chain 'C' and resid 2021 through 2036 removed outlier: 4.168A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2061 removed outlier: 3.850A pdb=" N VAL C2049 " --> pdb=" O SER C2045 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2120 Processing helix chain 'C' and resid 2148 through 2158 removed outlier: 3.788A pdb=" N LYS C2152 " --> pdb=" O THR C2148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C2157 " --> pdb=" O HIS C2153 " (cutoff:3.500A) Processing helix chain 'C' and resid 2168 through 2190 removed outlier: 4.182A pdb=" N PHE C2172 " --> pdb=" O VAL C2168 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP C2173 " --> pdb=" O SER C2169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C2174 " --> pdb=" O ASP C2170 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2194 through 2200 removed outlier: 4.261A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2200 through 2220 removed outlier: 4.401A pdb=" N TRP C2204 " --> pdb=" O ARG C2200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY C2205 " --> pdb=" O MET C2201 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER C2206 " --> pdb=" O THR C2202 " (cutoff:3.500A) Processing helix chain 'C' and resid 2238 through 2244 Processing helix chain 'C' and resid 2264 through 2275 Processing helix chain 'C' and resid 2277 through 2304 removed outlier: 3.561A pdb=" N ARG C2304 " --> pdb=" O PHE C2300 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2317 removed outlier: 3.780A pdb=" N MET C2316 " --> pdb=" O ALA C2313 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C2317 " --> pdb=" O MET C2314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2313 through 2317' Processing helix chain 'C' and resid 2319 through 2336 removed outlier: 3.880A pdb=" N HIS C2323 " --> pdb=" O GLU C2319 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'C' and resid 2340 through 2345 removed outlier: 3.836A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) Processing helix chain 'C' and resid 2347 through 2352 Processing helix chain 'C' and resid 2355 through 2364 removed outlier: 3.612A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2391 Processing helix chain 'C' and resid 2392 through 2395 removed outlier: 3.966A pdb=" N PHE C2395 " --> pdb=" O LYS C2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2392 through 2395' Processing helix chain 'C' and resid 2458 through 2471 removed outlier: 3.638A pdb=" N ILE C2462 " --> pdb=" O LEU C2458 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2505 Processing helix chain 'C' and resid 2509 through 2536 Processing helix chain 'C' and resid 2554 through 2559 Processing helix chain 'C' and resid 2564 through 2578 removed outlier: 4.014A pdb=" N TYR C2568 " --> pdb=" O ASN C2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C2569 " --> pdb=" O MET C2565 " (cutoff:3.500A) Processing helix chain 'C' and resid 2586 through 2596 removed outlier: 3.693A pdb=" N ASN C2596 " --> pdb=" O GLN C2592 " (cutoff:3.500A) Processing helix chain 'C' and resid 2623 through 2642 Processing helix chain 'D' and resid 51 through 54 removed outlier: 3.542A pdb=" N ASP D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.694A pdb=" N LYS D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 157 through 160 removed outlier: 3.589A pdb=" N SER D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 160' Processing helix chain 'D' and resid 362 through 365 removed outlier: 3.823A pdb=" N SER D 365 " --> pdb=" O ASP D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 435 through 462 removed outlier: 3.820A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 546 through 563 Processing helix chain 'D' and resid 567 through 577 removed outlier: 4.082A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 582 Processing helix chain 'D' and resid 583 through 585 No H-bonds generated for 'chain 'D' and resid 583 through 585' Processing helix chain 'D' and resid 590 through 599 removed outlier: 3.732A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR D 596 " --> pdb=" O GLU D 592 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 599 " --> pdb=" O ILE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 609 removed outlier: 3.853A pdb=" N LEU D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 626 removed outlier: 3.557A pdb=" N VAL D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN D 625 " --> pdb=" O LEU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 638 removed outlier: 3.717A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 633 " --> pdb=" O ARG D 629 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 634 " --> pdb=" O PHE D 630 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 739 Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.557A pdb=" N ILE D 751 " --> pdb=" O ALA D 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 752 " --> pdb=" O ILE D 748 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 764 removed outlier: 3.915A pdb=" N LEU D 759 " --> pdb=" O LEU D 755 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 761 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET D 764 " --> pdb=" O ILE D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 786 removed outlier: 3.824A pdb=" N ARG D 774 " --> pdb=" O PRO D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 819 removed outlier: 3.830A pdb=" N ASP D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER D 817 " --> pdb=" O LYS D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 846 Processing helix chain 'D' and resid 853 through 874 removed outlier: 3.667A pdb=" N PHE D 861 " --> pdb=" O ASN D 857 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 862 " --> pdb=" O LYS D 858 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 890 Processing helix chain 'D' and resid 962 through 1001 Processing helix chain 'D' and resid 1026 through 1035 Processing helix chain 'D' and resid 1051 through 1064 removed outlier: 3.673A pdb=" N PHE D1055 " --> pdb=" O GLY D1051 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D1058 " --> pdb=" O MET D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1082 removed outlier: 3.863A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1095 Processing helix chain 'D' and resid 1100 through 1127 Processing helix chain 'D' and resid 1171 through 1181 Processing helix chain 'D' and resid 1187 through 1200 Processing helix chain 'D' and resid 1202 through 1211 removed outlier: 3.823A pdb=" N MET D1206 " --> pdb=" O ALA D1202 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1236 Processing helix chain 'D' and resid 1239 through 1249 Processing helix chain 'D' and resid 1249 through 1254 removed outlier: 3.841A pdb=" N PHE D1253 " --> pdb=" O HIS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1268 removed outlier: 3.707A pdb=" N ALA D1261 " --> pdb=" O GLY D1257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) Processing helix chain 'D' and resid 1271 through 1276 Processing helix chain 'D' and resid 1279 through 1294 removed outlier: 3.532A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY D1294 " --> pdb=" O LEU D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1308 removed outlier: 3.768A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1328 removed outlier: 4.320A pdb=" N ASP D1319 " --> pdb=" O LYS D1315 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D1320 " --> pdb=" O LYS D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1344 removed outlier: 4.041A pdb=" N LEU D1342 " --> pdb=" O ASP D1338 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.545A pdb=" N ALA D1376 " --> pdb=" O LEU D1372 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1391 removed outlier: 3.527A pdb=" N GLU D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1392 through 1401 Processing helix chain 'D' and resid 1409 through 1416 removed outlier: 4.140A pdb=" N TYR D1413 " --> pdb=" O VAL D1409 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1477 Processing helix chain 'D' and resid 1588 through 1623 Proline residue: D1608 - end of helix Processing helix chain 'D' and resid 1624 through 1629 Processing helix chain 'D' and resid 1635 through 1639 Processing helix chain 'D' and resid 1642 through 1654 Processing helix chain 'D' and resid 1658 through 1673 removed outlier: 3.600A pdb=" N CYS D1662 " --> pdb=" O GLU D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1696 removed outlier: 3.885A pdb=" N GLN D1696 " --> pdb=" O GLN D1692 " (cutoff:3.500A) Processing helix chain 'D' and resid 1718 through 1731 Processing helix chain 'D' and resid 1732 through 1743 removed outlier: 3.541A pdb=" N LEU D1736 " --> pdb=" O GLY D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1746 through 1761 Processing helix chain 'D' and resid 1765 through 1778 removed outlier: 3.566A pdb=" N SER D1778 " --> pdb=" O ASN D1774 " (cutoff:3.500A) Processing helix chain 'D' and resid 1781 through 1803 Processing helix chain 'D' and resid 1864 through 1881 Proline residue: D1872 - end of helix removed outlier: 3.645A pdb=" N CYS D1881 " --> pdb=" O LEU D1877 " (cutoff:3.500A) Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1902 through 1916 Processing helix chain 'D' and resid 1922 through 1927 removed outlier: 3.521A pdb=" N LEU D1927 " --> pdb=" O GLY D1923 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1948 removed outlier: 3.610A pdb=" N VAL D1937 " --> pdb=" O ASN D1933 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS D1948 " --> pdb=" O LEU D1944 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1959 Processing helix chain 'D' and resid 1968 through 1976 Processing helix chain 'D' and resid 1981 through 1984 removed outlier: 4.118A pdb=" N TYR D1984 " --> pdb=" O LEU D1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1981 through 1984' Processing helix chain 'D' and resid 1985 through 2004 removed outlier: 4.042A pdb=" N VAL D1989 " --> pdb=" O ARG D1985 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2020 Processing helix chain 'D' and resid 2021 through 2036 removed outlier: 4.167A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2061 removed outlier: 3.850A pdb=" N VAL D2049 " --> pdb=" O SER D2045 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2120 Processing helix chain 'D' and resid 2148 through 2158 removed outlier: 3.789A pdb=" N LYS D2152 " --> pdb=" O THR D2148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D2157 " --> pdb=" O HIS D2153 " (cutoff:3.500A) Processing helix chain 'D' and resid 2168 through 2190 removed outlier: 4.182A pdb=" N PHE D2172 " --> pdb=" O VAL D2168 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP D2173 " --> pdb=" O SER D2169 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN D2174 " --> pdb=" O ASP D2170 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2194 through 2200 removed outlier: 4.261A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2200 through 2220 removed outlier: 4.400A pdb=" N TRP D2204 " --> pdb=" O ARG D2200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY D2205 " --> pdb=" O MET D2201 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER D2206 " --> pdb=" O THR D2202 " (cutoff:3.500A) Processing helix chain 'D' and resid 2238 through 2244 Processing helix chain 'D' and resid 2264 through 2275 Processing helix chain 'D' and resid 2277 through 2304 removed outlier: 3.562A pdb=" N ARG D2304 " --> pdb=" O PHE D2300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2317 removed outlier: 3.779A pdb=" N MET D2316 " --> pdb=" O ALA D2313 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D2317 " --> pdb=" O MET D2314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2313 through 2317' Processing helix chain 'D' and resid 2319 through 2336 removed outlier: 3.879A pdb=" N HIS D2323 " --> pdb=" O GLU D2319 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 2340 through 2345 removed outlier: 3.835A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) Processing helix chain 'D' and resid 2347 through 2352 Processing helix chain 'D' and resid 2355 through 2364 removed outlier: 3.612A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2391 Processing helix chain 'D' and resid 2392 through 2395 removed outlier: 3.966A pdb=" N PHE D2395 " --> pdb=" O LYS D2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2392 through 2395' Processing helix chain 'D' and resid 2458 through 2471 removed outlier: 3.638A pdb=" N ILE D2462 " --> pdb=" O LEU D2458 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2505 Processing helix chain 'D' and resid 2509 through 2536 Processing helix chain 'D' and resid 2554 through 2559 Processing helix chain 'D' and resid 2564 through 2578 removed outlier: 4.013A pdb=" N TYR D2568 " --> pdb=" O ASN D2564 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D2569 " --> pdb=" O MET D2565 " (cutoff:3.500A) Processing helix chain 'D' and resid 2586 through 2596 removed outlier: 3.694A pdb=" N ASN D2596 " --> pdb=" O GLN D2592 " (cutoff:3.500A) Processing helix chain 'D' and resid 2623 through 2642 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.057A pdb=" N CYS A 36 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 218 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER A 15 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU A 223 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 140 removed outlier: 4.043A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 251 removed outlier: 3.543A pdb=" N LYS A 250 " --> pdb=" O HIS A 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 257 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 317 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 Processing sheet with id=AA7, first strand: chain 'A' and resid 696 through 697 Processing sheet with id=AA8, first strand: chain 'A' and resid 800 through 801 removed outlier: 3.825A pdb=" N ARG A 801 " --> pdb=" O GLN A1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2122 through 2127 Processing sheet with id=AB1, first strand: chain 'A' and resid 2397 through 2398 Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.057A pdb=" N CYS B 36 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 218 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 15 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU B 223 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 140 removed outlier: 4.043A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 250 through 251 removed outlier: 3.543A pdb=" N LYS B 250 " --> pdb=" O HIS B 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 253 through 257 Processing sheet with id=AB6, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AB7, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AB8, first strand: chain 'B' and resid 696 through 697 Processing sheet with id=AB9, first strand: chain 'B' and resid 800 through 801 removed outlier: 3.826A pdb=" N ARG B 801 " --> pdb=" O GLN B1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 2122 through 2127 Processing sheet with id=AC2, first strand: chain 'B' and resid 2397 through 2398 Processing sheet with id=AC3, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.057A pdb=" N CYS C 36 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 218 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER C 15 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 223 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 132 through 140 removed outlier: 4.043A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.543A pdb=" N LYS C 250 " --> pdb=" O HIS C 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 253 through 257 Processing sheet with id=AC7, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AC8, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AC9, first strand: chain 'C' and resid 696 through 697 Processing sheet with id=AD1, first strand: chain 'C' and resid 800 through 801 removed outlier: 3.826A pdb=" N ARG C 801 " --> pdb=" O GLN C1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 2122 through 2127 Processing sheet with id=AD3, first strand: chain 'C' and resid 2397 through 2398 Processing sheet with id=AD4, first strand: chain 'D' and resid 194 through 196 removed outlier: 6.057A pdb=" N CYS D 36 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 218 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER D 15 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D 223 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 132 through 140 removed outlier: 4.044A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.543A pdb=" N LYS D 250 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 257 Processing sheet with id=AD8, first strand: chain 'D' and resid 314 through 317 Processing sheet with id=AD9, first strand: chain 'D' and resid 397 through 399 Processing sheet with id=AE1, first strand: chain 'D' and resid 696 through 697 Processing sheet with id=AE2, first strand: chain 'D' and resid 800 through 801 removed outlier: 3.826A pdb=" N ARG D 801 " --> pdb=" O GLN D1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 2122 through 2127 Processing sheet with id=AE4, first strand: chain 'D' and resid 2397 through 2398 3620 hydrogen bonds defined for protein. 10656 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: 30.52 Time building geometry restraints manager: 22.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18135 1.34 - 1.46: 10865 1.46 - 1.58: 23483 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 52571 Sorted by residual: bond pdb=" C LEU D 139 " pdb=" N PRO D 140 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.25e-02 6.40e+03 2.75e+00 bond pdb=" C LEU A 139 " pdb=" N PRO A 140 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.25e-02 6.40e+03 2.71e+00 bond pdb=" C LEU B 139 " pdb=" N PRO B 140 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.25e-02 6.40e+03 2.58e+00 bond pdb=" C LEU C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.25e-02 6.40e+03 2.56e+00 bond pdb=" C LEU A 769 " pdb=" N PRO A 770 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 52566 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 1315 107.18 - 113.89: 28608 113.89 - 120.60: 21884 120.60 - 127.31: 19943 127.31 - 134.02: 548 Bond angle restraints: 72298 Sorted by residual: angle pdb=" CA ILE C 589 " pdb=" CB ILE C 589 " pdb=" CG1 ILE C 589 " ideal model delta sigma weight residual 110.40 114.44 -4.04 1.70e+00 3.46e-01 5.64e+00 angle pdb=" CA ILE D 589 " pdb=" CB ILE D 589 " pdb=" CG1 ILE D 589 " ideal model delta sigma weight residual 110.40 114.42 -4.02 1.70e+00 3.46e-01 5.59e+00 angle pdb=" CA ILE A 589 " pdb=" CB ILE A 589 " pdb=" CG1 ILE A 589 " ideal model delta sigma weight residual 110.40 114.39 -3.99 1.70e+00 3.46e-01 5.52e+00 angle pdb=" CA ILE B 589 " pdb=" CB ILE B 589 " pdb=" CG1 ILE B 589 " ideal model delta sigma weight residual 110.40 114.39 -3.99 1.70e+00 3.46e-01 5.50e+00 angle pdb=" N GLN D 491 " pdb=" CA GLN D 491 " pdb=" C GLN D 491 " ideal model delta sigma weight residual 110.80 115.78 -4.98 2.13e+00 2.20e-01 5.46e+00 ... (remaining 72293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 29119 17.57 - 35.14: 987 35.14 - 52.71: 136 52.71 - 70.28: 12 70.28 - 87.85: 24 Dihedral angle restraints: 30278 sinusoidal: 6216 harmonic: 24062 Sorted by residual: dihedral pdb=" CA LEU A 769 " pdb=" C LEU A 769 " pdb=" N PRO A 770 " pdb=" CA PRO A 770 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU B 769 " pdb=" C LEU B 769 " pdb=" N PRO B 770 " pdb=" CA PRO B 770 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU C 769 " pdb=" C LEU C 769 " pdb=" N PRO C 770 " pdb=" CA PRO C 770 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 30275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6031 0.031 - 0.062: 1549 0.062 - 0.094: 774 0.094 - 0.125: 206 0.125 - 0.156: 35 Chirality restraints: 8595 Sorted by residual: chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE C 806 " pdb=" N ILE C 806 " pdb=" C ILE C 806 " pdb=" CB ILE C 806 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE B 806 " pdb=" N ILE B 806 " pdb=" C ILE B 806 " pdb=" CB ILE B 806 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 8592 not shown) Planarity restraints: 9760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 769 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 770 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 770 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 770 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 769 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO B 770 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 769 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO C 770 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 770 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 770 " -0.022 5.00e-02 4.00e+02 ... (remaining 9757 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 19585 2.89 - 3.39: 49163 3.39 - 3.90: 77201 3.90 - 4.40: 74190 4.40 - 4.90: 129549 Nonbonded interactions: 349688 Sorted by model distance: nonbonded pdb=" O ASP C1048 " pdb=" N GLY C1051 " model vdw 2.388 2.520 nonbonded pdb=" O ASP D1048 " pdb=" N GLY D1051 " model vdw 2.388 2.520 nonbonded pdb=" O ASP A1048 " pdb=" N GLY A1051 " model vdw 2.389 2.520 nonbonded pdb=" O ASP B1048 " pdb=" N GLY B1051 " model vdw 2.389 2.520 nonbonded pdb=" O LEU A2155 " pdb=" OG1 THR A2159 " model vdw 2.416 2.440 ... (remaining 349683 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 'A' selection = (chain 'B' and (resid 5 through 1886 or (resid 1887 and (name N or name CA or na \ me C or name O )) or resid 1888 through 2642 or resid 4000)) selection = (chain 'C' and (resid 5 through 1886 or (resid 1887 and (name N or name CA or na \ me C or name O )) or resid 1888 through 2642 or resid 4000)) selection = (chain 'D' and (resid 5 through 1886 or (resid 1887 and (name N or name CA or na \ me C or name O )) or resid 1888 through 2642 or resid 4000)) } 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: 1.610 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: 0.040 Extract box with map and model: 12.010 Check model and map are aligned: 0.760 Set scattering table: 0.520 Process input model: 153.240 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.350 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.003 0.026 52571 Z= 0.177 Angle : 0.533 6.810 72298 Z= 0.286 Chirality : 0.037 0.156 8595 Planarity : 0.003 0.039 9760 Dihedral : 9.909 87.854 14560 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.09), residues: 7856 helix: -0.07 (0.07), residues: 4652 sheet: -1.64 (0.22), residues: 500 loop : -3.19 (0.09), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1127 HIS 0.003 0.000 HIS A2468 PHE 0.009 0.001 PHE B2502 TYR 0.015 0.001 TYR A2583 ARG 0.007 0.001 ARG B2524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 803 time to evaluate : 5.982 Fit side-chains revert: symmetry clash REVERT: A 411 ARG cc_start: 0.8806 (ttm170) cc_final: 0.8547 (mmm-85) REVERT: A 457 GLU cc_start: 0.8930 (tp30) cc_final: 0.8641 (tp30) REVERT: A 1227 TYR cc_start: 0.8887 (m-80) cc_final: 0.8291 (m-80) REVERT: A 2184 TRP cc_start: 0.8782 (t-100) cc_final: 0.8424 (t-100) REVERT: A 2360 LYS cc_start: 0.6939 (mttt) cc_final: 0.6717 (mmtt) REVERT: A 2531 GLU cc_start: 0.9103 (tp30) cc_final: 0.8897 (tp30) REVERT: A 2593 MET cc_start: 0.8931 (mmm) cc_final: 0.8209 (tpp) REVERT: B 457 GLU cc_start: 0.9007 (tp30) cc_final: 0.8725 (tp30) REVERT: B 1227 TYR cc_start: 0.8893 (m-80) cc_final: 0.8258 (m-80) REVERT: B 2184 TRP cc_start: 0.8726 (t-100) cc_final: 0.8297 (t-100) REVERT: B 2360 LYS cc_start: 0.7246 (mttt) cc_final: 0.6935 (mmtt) REVERT: B 2593 MET cc_start: 0.8936 (mmm) cc_final: 0.8148 (tpp) REVERT: C 457 GLU cc_start: 0.9105 (tp30) cc_final: 0.8815 (tp30) REVERT: C 1227 TYR cc_start: 0.9017 (m-80) cc_final: 0.8414 (m-80) REVERT: C 2174 GLN cc_start: 0.8610 (mm110) cc_final: 0.8401 (mm-40) REVERT: C 2184 TRP cc_start: 0.8739 (t-100) cc_final: 0.8476 (t-100) REVERT: C 2197 PHE cc_start: 0.8882 (t80) cc_final: 0.8069 (t80) REVERT: C 2528 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8742 (tm-30) REVERT: C 2531 GLU cc_start: 0.9153 (tp30) cc_final: 0.8913 (tp30) REVERT: C 2532 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 457 GLU cc_start: 0.9103 (tp30) cc_final: 0.8833 (tp30) REVERT: D 582 GLN cc_start: 0.9004 (pt0) cc_final: 0.8758 (pt0) REVERT: D 1227 TYR cc_start: 0.9060 (m-80) cc_final: 0.8518 (m-80) REVERT: D 2184 TRP cc_start: 0.8740 (t-100) cc_final: 0.8288 (t-100) REVERT: D 2197 PHE cc_start: 0.8812 (t80) cc_final: 0.8183 (t80) REVERT: D 2360 LYS cc_start: 0.7244 (mttt) cc_final: 0.6920 (mmtt) REVERT: D 2379 LEU cc_start: 0.9434 (tp) cc_final: 0.9041 (tp) REVERT: D 2593 MET cc_start: 0.8892 (mmm) cc_final: 0.8136 (tpp) outliers start: 0 outliers final: 0 residues processed: 803 average time/residue: 0.5644 time to fit residues: 769.7946 Evaluate side-chains 515 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 692 optimal weight: 10.0000 chunk 621 optimal weight: 3.9990 chunk 344 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 642 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 390 optimal weight: 9.9990 chunk 478 optimal weight: 20.0000 chunk 744 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 204 ASN A 226 GLN A 230 HIS A 245 HIS A 391 HIS A 517 GLN A 571 GLN A 783 HIS A 868 HIS A1249 HIS A2119 ASN A2120 HIS B 101 GLN B 204 ASN B 226 GLN B 230 HIS B 245 HIS B 391 HIS B 517 GLN B 571 GLN B 649 GLN B 783 HIS B 868 HIS B1249 HIS ** B2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN C 204 ASN C 226 GLN C 230 HIS ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 391 HIS C 517 GLN C 571 GLN C 649 GLN C 783 HIS C 868 HIS C1249 HIS C2051 HIS ** C2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 204 ASN D 226 GLN D 230 HIS D 245 HIS D 391 HIS D 517 GLN D 571 GLN D 649 GLN D 783 HIS D 868 HIS D1249 HIS ** D2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 52571 Z= 0.485 Angle : 0.719 10.111 72298 Z= 0.402 Chirality : 0.044 0.186 8595 Planarity : 0.005 0.099 9760 Dihedral : 4.780 28.829 8576 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.61 % Favored : 92.38 % Rotamer: Outliers : 3.12 % Allowed : 10.83 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.10), residues: 7856 helix: 0.96 (0.08), residues: 4712 sheet: -1.37 (0.22), residues: 532 loop : -2.85 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C2204 HIS 0.016 0.002 HIS A2153 PHE 0.024 0.003 PHE C2513 TYR 0.033 0.003 TYR A2568 ARG 0.010 0.001 ARG B1792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 429 time to evaluate : 6.052 Fit side-chains REVERT: A 148 MET cc_start: 0.8909 (mpp) cc_final: 0.8477 (mtp) REVERT: A 457 GLU cc_start: 0.9090 (tp30) cc_final: 0.8747 (tp30) REVERT: A 1227 TYR cc_start: 0.8899 (m-80) cc_final: 0.8297 (m-80) REVERT: A 2528 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8741 (tm-30) REVERT: B 148 MET cc_start: 0.8913 (mpp) cc_final: 0.8431 (mtp) REVERT: B 457 GLU cc_start: 0.9077 (tp30) cc_final: 0.8775 (tp30) REVERT: B 1227 TYR cc_start: 0.8932 (m-80) cc_final: 0.8227 (m-80) REVERT: B 2182 MET cc_start: 0.9213 (mtm) cc_final: 0.8998 (mtp) REVERT: B 2518 ASP cc_start: 0.8982 (m-30) cc_final: 0.8604 (m-30) REVERT: B 2520 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8508 (t80) REVERT: B 2532 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8513 (tm-30) REVERT: C 457 GLU cc_start: 0.9102 (tp30) cc_final: 0.8794 (tp30) REVERT: C 1227 TYR cc_start: 0.8965 (m-80) cc_final: 0.8241 (m-80) REVERT: C 2518 ASP cc_start: 0.8910 (m-30) cc_final: 0.8211 (m-30) REVERT: C 2528 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8749 (tm-30) REVERT: C 2593 MET cc_start: 0.9270 (tpp) cc_final: 0.8218 (mpp) REVERT: D 148 MET cc_start: 0.8889 (mpp) cc_final: 0.8268 (mtp) REVERT: D 457 GLU cc_start: 0.9114 (tp30) cc_final: 0.8807 (tp30) REVERT: D 1227 TYR cc_start: 0.9033 (m-80) cc_final: 0.8379 (m-80) REVERT: D 2371 LEU cc_start: 0.8992 (tp) cc_final: 0.8485 (tp) REVERT: D 2518 ASP cc_start: 0.8972 (m-30) cc_final: 0.8655 (m-30) REVERT: D 2532 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8468 (tm-30) outliers start: 83 outliers final: 37 residues processed: 499 average time/residue: 0.4846 time to fit residues: 443.7235 Evaluate side-chains 428 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 390 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2362 VAL Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2505 ILE Chi-restraints excluded: chain B residue 2515 VAL Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2012 ASN Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 556 CYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2362 VAL Chi-restraints excluded: chain D residue 2394 ASP Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2505 ILE Chi-restraints excluded: chain D residue 2515 VAL Chi-restraints excluded: chain D residue 2519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 413 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 619 optimal weight: 0.0470 chunk 507 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 745 optimal weight: 20.0000 chunk 805 optimal weight: 0.0770 chunk 664 optimal weight: 9.9990 chunk 739 optimal weight: 9.9990 chunk 254 optimal weight: 0.0070 chunk 598 optimal weight: 1.9990 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 HIS B 783 HIS C 245 HIS C 783 HIS D 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 52571 Z= 0.137 Angle : 0.449 8.101 72298 Z= 0.240 Chirality : 0.038 0.156 8595 Planarity : 0.003 0.090 9760 Dihedral : 3.710 28.737 8576 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.63 % Allowed : 13.20 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.10), residues: 7856 helix: 1.91 (0.08), residues: 4676 sheet: -0.82 (0.25), residues: 484 loop : -2.55 (0.11), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D2566 HIS 0.005 0.001 HIS B2558 PHE 0.018 0.001 PHE B2520 TYR 0.015 0.001 TYR B2033 ARG 0.007 0.000 ARG A2471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 474 time to evaluate : 6.122 Fit side-chains REVERT: A 148 MET cc_start: 0.8851 (mpp) cc_final: 0.8556 (mtp) REVERT: A 457 GLU cc_start: 0.9049 (tp30) cc_final: 0.8737 (tp30) REVERT: A 1227 TYR cc_start: 0.8906 (m-80) cc_final: 0.8298 (m-80) REVERT: A 1772 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8430 (t80) REVERT: B 148 MET cc_start: 0.8811 (mpp) cc_final: 0.8469 (mtp) REVERT: B 457 GLU cc_start: 0.9036 (tp30) cc_final: 0.8733 (tp30) REVERT: B 1227 TYR cc_start: 0.8937 (m-80) cc_final: 0.8208 (m-80) REVERT: B 1772 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8477 (t80) REVERT: B 2182 MET cc_start: 0.9057 (mtm) cc_final: 0.8785 (mtp) REVERT: B 2320 PHE cc_start: 0.9081 (t80) cc_final: 0.8877 (t80) REVERT: B 2371 LEU cc_start: 0.9017 (tp) cc_final: 0.8343 (tp) REVERT: B 2381 TYR cc_start: 0.8974 (t80) cc_final: 0.8370 (t80) REVERT: B 2532 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 148 MET cc_start: 0.8797 (mpp) cc_final: 0.8274 (mtp) REVERT: C 195 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8543 (t70) REVERT: C 457 GLU cc_start: 0.9058 (tp30) cc_final: 0.8757 (tp30) REVERT: C 1227 TYR cc_start: 0.8935 (m-80) cc_final: 0.8208 (m-80) REVERT: C 1772 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8401 (t80) REVERT: C 2518 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: C 2593 MET cc_start: 0.9295 (tpp) cc_final: 0.8551 (mmm) REVERT: D 148 MET cc_start: 0.8716 (mpp) cc_final: 0.8198 (mtp) REVERT: D 195 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8456 (t70) REVERT: D 457 GLU cc_start: 0.9055 (tp30) cc_final: 0.8765 (tp30) REVERT: D 1227 TYR cc_start: 0.9027 (m-80) cc_final: 0.8361 (m-80) REVERT: D 1772 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8426 (t80) REVERT: D 2518 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8644 (m-30) outliers start: 70 outliers final: 41 residues processed: 526 average time/residue: 0.5114 time to fit residues: 488.8582 Evaluate side-chains 487 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 438 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 1266 HIS Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2340 PHE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2505 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2362 VAL Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2505 ILE Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 1266 HIS Chi-restraints excluded: chain C residue 1293 HIS Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2012 ASN Chi-restraints excluded: chain C residue 2340 PHE Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 557 TYR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 1293 HIS Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2394 ASP Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 737 optimal weight: 9.9990 chunk 560 optimal weight: 9.9990 chunk 387 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 500 optimal weight: 10.0000 chunk 748 optimal weight: 10.0000 chunk 792 optimal weight: 9.9990 chunk 391 optimal weight: 0.1980 chunk 709 optimal weight: 30.0000 chunk 213 optimal weight: 4.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS A 783 HIS A1296 HIS B 230 HIS B 721 HIS B 783 HIS B1296 HIS B2120 HIS C 783 HIS C1296 HIS C2120 HIS D 783 HIS D2120 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 52571 Z= 0.334 Angle : 0.570 9.614 72298 Z= 0.310 Chirality : 0.041 0.146 8595 Planarity : 0.004 0.098 9760 Dihedral : 4.101 29.488 8576 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.95 % Allowed : 15.34 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7856 helix: 1.91 (0.08), residues: 4760 sheet: -0.65 (0.25), residues: 484 loop : -2.72 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D2566 HIS 0.007 0.001 HIS C2558 PHE 0.022 0.002 PHE C1286 TYR 0.027 0.002 TYR D2568 ARG 0.008 0.001 ARG B2493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 425 time to evaluate : 5.590 Fit side-chains REVERT: A 148 MET cc_start: 0.8943 (mpp) cc_final: 0.8551 (mtp) REVERT: A 195 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8622 (t70) REVERT: A 457 GLU cc_start: 0.9100 (tp30) cc_final: 0.8777 (tp30) REVERT: A 1227 TYR cc_start: 0.8916 (m-80) cc_final: 0.8269 (m-80) REVERT: A 1772 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8459 (t80) REVERT: A 2518 ASP cc_start: 0.8914 (m-30) cc_final: 0.8398 (m-30) REVERT: A 2520 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8635 (t80) REVERT: B 148 MET cc_start: 0.8944 (mpp) cc_final: 0.8718 (mtm) REVERT: B 195 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8638 (t70) REVERT: B 457 GLU cc_start: 0.9070 (tp30) cc_final: 0.8782 (tp30) REVERT: B 1227 TYR cc_start: 0.8943 (m-80) cc_final: 0.8218 (m-80) REVERT: B 1772 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8461 (t80) REVERT: B 1911 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9081 (tt) REVERT: B 2184 TRP cc_start: 0.8482 (t-100) cc_final: 0.8262 (t60) REVERT: B 2518 ASP cc_start: 0.8832 (m-30) cc_final: 0.8461 (m-30) REVERT: B 2520 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 2532 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 148 MET cc_start: 0.8940 (mpp) cc_final: 0.8177 (mtp) REVERT: C 195 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8621 (t70) REVERT: C 451 MET cc_start: 0.9361 (tpp) cc_final: 0.9158 (tpp) REVERT: C 457 GLU cc_start: 0.9083 (tp30) cc_final: 0.8796 (tp30) REVERT: C 1227 TYR cc_start: 0.8955 (m-80) cc_final: 0.8224 (m-80) REVERT: C 1260 GLU cc_start: 0.7876 (tt0) cc_final: 0.7509 (tt0) REVERT: C 1772 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8400 (t80) REVERT: C 2518 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: C 2520 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8663 (t80) REVERT: C 2532 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8318 (tm-30) REVERT: D 148 MET cc_start: 0.8871 (mpp) cc_final: 0.8235 (mtp) REVERT: D 195 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8591 (t70) REVERT: D 451 MET cc_start: 0.9348 (tpp) cc_final: 0.9124 (tpp) REVERT: D 457 GLU cc_start: 0.9100 (tp30) cc_final: 0.8808 (tp30) REVERT: D 1227 TYR cc_start: 0.8997 (m-80) cc_final: 0.8331 (m-80) REVERT: D 1260 GLU cc_start: 0.7809 (tt0) cc_final: 0.7463 (tt0) REVERT: D 1772 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8458 (t80) REVERT: D 2371 LEU cc_start: 0.9171 (tp) cc_final: 0.8496 (tp) REVERT: D 2518 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: D 2520 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8600 (t80) outliers start: 105 outliers final: 63 residues processed: 502 average time/residue: 0.4966 time to fit residues: 461.0299 Evaluate side-chains 489 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 411 time to evaluate : 5.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1268 PHE Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2340 PHE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2505 ILE Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2340 PHE Chi-restraints excluded: chain B residue 2346 PHE Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2505 ILE Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 1268 PHE Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2012 ASN Chi-restraints excluded: chain C residue 2340 PHE Chi-restraints excluded: chain C residue 2346 PHE Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2468 HIS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 557 TYR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 778 CYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2119 ASN Chi-restraints excluded: chain D residue 2340 PHE Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2505 ILE Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2520 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 660 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 590 optimal weight: 0.0170 chunk 327 optimal weight: 7.9990 chunk 676 optimal weight: 3.9990 chunk 547 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 404 optimal weight: 0.9990 chunk 711 optimal weight: 50.0000 chunk 200 optimal weight: 9.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52571 Z= 0.270 Angle : 0.524 8.688 72298 Z= 0.283 Chirality : 0.040 0.150 8595 Planarity : 0.004 0.095 9760 Dihedral : 3.987 29.064 8576 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.51 % Allowed : 15.71 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 7856 helix: 2.08 (0.08), residues: 4728 sheet: -0.60 (0.26), residues: 484 loop : -2.62 (0.11), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C2566 HIS 0.014 0.001 HIS B 230 PHE 0.033 0.001 PHE A1286 TYR 0.022 0.001 TYR D2568 ARG 0.006 0.000 ARG B2493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 428 time to evaluate : 5.836 Fit side-chains REVERT: A 148 MET cc_start: 0.8963 (mpp) cc_final: 0.8571 (mtp) REVERT: A 457 GLU cc_start: 0.9105 (tp30) cc_final: 0.8783 (tp30) REVERT: A 1227 TYR cc_start: 0.8935 (m-80) cc_final: 0.8268 (m-80) REVERT: A 1772 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8456 (t80) REVERT: A 2518 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: A 2520 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8629 (t80) REVERT: B 148 MET cc_start: 0.8965 (mpp) cc_final: 0.8758 (mtm) REVERT: B 195 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (t70) REVERT: B 457 GLU cc_start: 0.9044 (tp30) cc_final: 0.8753 (tp30) REVERT: B 459 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9072 (tt) REVERT: B 1227 TYR cc_start: 0.8944 (m-80) cc_final: 0.8198 (m-80) REVERT: B 1772 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8453 (t80) REVERT: B 2518 ASP cc_start: 0.8924 (m-30) cc_final: 0.8455 (m-30) REVERT: B 2520 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 2532 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8424 (tm-30) REVERT: C 148 MET cc_start: 0.8987 (mpp) cc_final: 0.8732 (mtm) REVERT: C 195 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (t70) REVERT: C 457 GLU cc_start: 0.9054 (tp30) cc_final: 0.8764 (tp30) REVERT: C 1227 TYR cc_start: 0.8956 (m-80) cc_final: 0.8206 (m-80) REVERT: C 1260 GLU cc_start: 0.7742 (tt0) cc_final: 0.7364 (tt0) REVERT: C 1772 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8466 (t80) REVERT: C 2518 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: C 2520 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8708 (t80) REVERT: C 2532 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 148 MET cc_start: 0.8863 (mpp) cc_final: 0.8243 (mtp) REVERT: D 195 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8581 (t70) REVERT: D 457 GLU cc_start: 0.9086 (tp30) cc_final: 0.8802 (tp30) REVERT: D 1227 TYR cc_start: 0.9001 (m-80) cc_final: 0.8338 (m-80) REVERT: D 1260 GLU cc_start: 0.7798 (tt0) cc_final: 0.7388 (tt0) REVERT: D 1772 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8481 (t80) REVERT: D 2518 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8460 (m-30) REVERT: D 2520 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8592 (t80) REVERT: D 2532 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8442 (tm-30) outliers start: 120 outliers final: 74 residues processed: 522 average time/residue: 0.4964 time to fit residues: 480.5610 Evaluate side-chains 508 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 419 time to evaluate : 6.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1266 HIS Chi-restraints excluded: chain A residue 1268 PHE Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2340 PHE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2386 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2518 ASP Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 1266 HIS Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1293 HIS Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2340 PHE Chi-restraints excluded: chain B residue 2346 PHE Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 778 CYS Chi-restraints excluded: chain C residue 1268 PHE Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2340 PHE Chi-restraints excluded: chain C residue 2346 PHE Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2468 HIS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 557 TYR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 778 CYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2119 ASN Chi-restraints excluded: chain D residue 2340 PHE Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2520 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 266 optimal weight: 5.9990 chunk 713 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 465 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 793 optimal weight: 9.9990 chunk 658 optimal weight: 1.9990 chunk 367 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 416 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS B 126 HIS B 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 52571 Z= 0.222 Angle : 0.491 7.986 72298 Z= 0.264 Chirality : 0.039 0.152 8595 Planarity : 0.003 0.098 9760 Dihedral : 3.813 29.243 8576 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.74 % Allowed : 16.17 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.10), residues: 7856 helix: 2.28 (0.08), residues: 4732 sheet: -0.64 (0.26), residues: 484 loop : -2.48 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D2184 HIS 0.008 0.001 HIS B 230 PHE 0.022 0.001 PHE A1286 TYR 0.019 0.001 TYR D2568 ARG 0.005 0.000 ARG A2471 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 428 time to evaluate : 6.127 Fit side-chains REVERT: A 148 MET cc_start: 0.8869 (mpp) cc_final: 0.8521 (mtp) REVERT: A 457 GLU cc_start: 0.9099 (tp30) cc_final: 0.8789 (tp30) REVERT: A 1227 TYR cc_start: 0.8932 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1772 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8451 (t80) REVERT: A 2182 MET cc_start: 0.9170 (mtm) cc_final: 0.8922 (mtp) REVERT: A 2518 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: A 2520 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8510 (t80) REVERT: A 2532 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 148 MET cc_start: 0.8912 (mpp) cc_final: 0.8705 (mtm) REVERT: B 457 GLU cc_start: 0.9035 (tp30) cc_final: 0.8739 (tp30) REVERT: B 459 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9050 (tt) REVERT: B 1227 TYR cc_start: 0.8946 (m-80) cc_final: 0.8199 (m-80) REVERT: B 1772 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8450 (t80) REVERT: B 2371 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8235 (tp) REVERT: B 2518 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: B 2520 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8640 (t80) REVERT: B 2532 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 148 MET cc_start: 0.8913 (mpp) cc_final: 0.8386 (mtp) REVERT: C 195 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8564 (t70) REVERT: C 457 GLU cc_start: 0.9030 (tp30) cc_final: 0.8743 (tp30) REVERT: C 1227 TYR cc_start: 0.8958 (m-80) cc_final: 0.8205 (m-80) REVERT: C 1772 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8442 (t80) REVERT: C 2182 MET cc_start: 0.9206 (mtm) cc_final: 0.8991 (mtp) REVERT: C 2518 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: C 2520 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8646 (t80) REVERT: C 2532 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 111 VAL cc_start: 0.9075 (t) cc_final: 0.8872 (p) REVERT: D 195 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8567 (t70) REVERT: D 457 GLU cc_start: 0.9077 (tp30) cc_final: 0.8794 (tp30) REVERT: D 778 CYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8563 (m) REVERT: D 1227 TYR cc_start: 0.9000 (m-80) cc_final: 0.8333 (m-80) REVERT: D 1772 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8451 (t80) REVERT: D 2182 MET cc_start: 0.9197 (mtm) cc_final: 0.8886 (mtp) REVERT: D 2518 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: D 2520 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8582 (t80) REVERT: D 2532 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 126 outliers final: 77 residues processed: 526 average time/residue: 0.4926 time to fit residues: 478.5776 Evaluate side-chains 513 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 419 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1266 HIS Chi-restraints excluded: chain A residue 1268 PHE Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2340 PHE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2386 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2518 ASP Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 1266 HIS Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2340 PHE Chi-restraints excluded: chain B residue 2346 PHE Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 778 CYS Chi-restraints excluded: chain C residue 1268 PHE Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2012 ASN Chi-restraints excluded: chain C residue 2340 PHE Chi-restraints excluded: chain C residue 2346 PHE Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2386 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2468 HIS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 557 TYR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 778 CYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 1268 PHE Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2119 ASN Chi-restraints excluded: chain D residue 2340 PHE Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2520 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 764 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 452 optimal weight: 7.9990 chunk 579 optimal weight: 7.9990 chunk 448 optimal weight: 6.9990 chunk 667 optimal weight: 0.9990 chunk 443 optimal weight: 7.9990 chunk 790 optimal weight: 20.0000 chunk 494 optimal weight: 5.9990 chunk 481 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 HIS C2472 ASN D 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 52571 Z= 0.387 Angle : 0.613 8.428 72298 Z= 0.335 Chirality : 0.042 0.154 8595 Planarity : 0.004 0.100 9760 Dihedral : 4.390 28.756 8576 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.92 % Allowed : 16.69 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7856 helix: 1.94 (0.08), residues: 4724 sheet: -0.78 (0.26), residues: 468 loop : -2.61 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D2184 HIS 0.009 0.001 HIS B 230 PHE 0.025 0.002 PHE C1286 TYR 0.029 0.002 TYR C2568 ARG 0.005 0.000 ARG B2493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15712 Ramachandran restraints generated. 7856 Oldfield, 0 Emsley, 7856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 399 time to evaluate : 6.142 Fit side-chains REVERT: A 457 GLU cc_start: 0.9116 (tp30) cc_final: 0.8815 (tp30) REVERT: A 1227 TYR cc_start: 0.8946 (m-80) cc_final: 0.8252 (m-80) REVERT: A 1772 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8458 (t80) REVERT: A 2182 MET cc_start: 0.9162 (mtm) cc_final: 0.8886 (mtp) REVERT: A 2388 PHE cc_start: 0.8963 (t80) cc_final: 0.8759 (t80) REVERT: A 2518 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: A 2520 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8585 (t80) REVERT: A 2532 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 195 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8616 (t70) REVERT: B 457 GLU cc_start: 0.9128 (tp30) cc_final: 0.8829 (tp30) REVERT: B 459 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8918 (tt) REVERT: B 1227 TYR cc_start: 0.8944 (m-80) cc_final: 0.8207 (m-80) REVERT: B 1772 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8452 (t80) REVERT: B 2518 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: B 2520 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8508 (t80) REVERT: B 2531 GLU cc_start: 0.9356 (tp30) cc_final: 0.8898 (tm-30) REVERT: C 148 MET cc_start: 0.8963 (mpp) cc_final: 0.8759 (mtm) REVERT: C 457 GLU cc_start: 0.9107 (tp30) cc_final: 0.8801 (tp30) REVERT: C 1227 TYR cc_start: 0.9004 (m-80) cc_final: 0.8311 (m-80) REVERT: C 1772 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8449 (t80) REVERT: C 2182 MET cc_start: 0.9243 (mtm) cc_final: 0.8995 (mtp) REVERT: C 2518 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: C 2520 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8580 (t80) REVERT: C 2532 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 195 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8677 (t70) REVERT: D 457 GLU cc_start: 0.9058 (tp30) cc_final: 0.8776 (tp30) REVERT: D 1227 TYR cc_start: 0.8998 (m-80) cc_final: 0.8328 (m-80) REVERT: D 1772 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8457 (t80) REVERT: D 2518 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: D 2520 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8592 (t80) REVERT: D 2531 GLU cc_start: 0.9358 (tp30) cc_final: 0.8897 (tm-30) outliers start: 131 outliers final: 84 residues processed: 497 average time/residue: 0.5538 time to fit residues: 514.0702 Evaluate side-chains 492 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 393 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1268 PHE Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 2012 ASN Chi-restraints excluded: chain A residue 2340 PHE Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2386 VAL Chi-restraints excluded: chain A residue 2462 ILE Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2518 ASP Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 778 CYS Chi-restraints excluded: chain B residue 1268 PHE Chi-restraints excluded: chain B residue 1772 PHE Chi-restraints excluded: chain B residue 2012 ASN Chi-restraints excluded: chain B residue 2197 PHE Chi-restraints excluded: chain B residue 2340 PHE Chi-restraints excluded: chain B residue 2346 PHE Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2462 ILE Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 778 CYS Chi-restraints excluded: chain C residue 1268 PHE Chi-restraints excluded: chain C residue 1772 PHE Chi-restraints excluded: chain C residue 2012 ASN Chi-restraints excluded: chain C residue 2340 PHE Chi-restraints excluded: chain C residue 2346 PHE Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2386 VAL Chi-restraints excluded: chain C residue 2462 ILE Chi-restraints excluded: chain C residue 2472 ASN Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 230 HIS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 557 TYR Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 778 CYS Chi-restraints excluded: chain D residue 865 SER Chi-restraints excluded: chain D residue 1268 PHE Chi-restraints excluded: chain D residue 1772 PHE Chi-restraints excluded: chain D residue 2012 ASN Chi-restraints excluded: chain D residue 2119 ASN Chi-restraints excluded: chain D residue 2340 PHE Chi-restraints excluded: chain D residue 2346 PHE Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2462 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2520 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 66.0245 > 50: distance: 7 - 22: 36.193 distance: 12 - 27: 29.247 distance: 19 - 22: 34.360 distance: 22 - 23: 44.967 distance: 23 - 24: 15.076 distance: 23 - 26: 44.662 distance: 24 - 25: 26.043 distance: 24 - 27: 43.127 distance: 27 - 28: 17.956 distance: 28 - 29: 19.725 distance: 28 - 31: 13.423 distance: 29 - 30: 5.562 distance: 29 - 32: 20.494 distance: 32 - 33: 51.181 distance: 33 - 34: 19.088 distance: 33 - 36: 20.911 distance: 34 - 35: 39.524 distance: 34 - 37: 35.450 distance: 35 - 54: 18.426 distance: 37 - 38: 29.038 distance: 37 - 43: 25.117 distance: 38 - 39: 12.817 distance: 39 - 40: 26.050 distance: 39 - 44: 8.410 distance: 40 - 59: 16.619 distance: 41 - 42: 10.863 distance: 42 - 43: 9.532 distance: 44 - 45: 22.311 distance: 45 - 46: 15.355 distance: 45 - 48: 45.130 distance: 46 - 47: 40.051 distance: 46 - 49: 52.739 distance: 47 - 64: 20.902 distance: 49 - 50: 39.709 distance: 50 - 51: 47.333 distance: 50 - 53: 4.097 distance: 51 - 52: 14.610 distance: 51 - 54: 53.653 distance: 52 - 69: 33.030 distance: 54 - 55: 14.670 distance: 55 - 56: 23.863 distance: 55 - 58: 49.361 distance: 56 - 57: 43.914 distance: 56 - 59: 22.198 distance: 57 - 74: 35.277 distance: 59 - 60: 26.516 distance: 60 - 61: 12.459 distance: 60 - 63: 13.197 distance: 61 - 62: 26.845 distance: 61 - 64: 15.808 distance: 62 - 79: 22.000 distance: 64 - 65: 9.436 distance: 65 - 66: 11.511 distance: 66 - 67: 14.991 distance: 66 - 69: 37.523 distance: 67 - 84: 31.283 distance: 69 - 70: 23.333 distance: 70 - 71: 22.167 distance: 70 - 73: 27.768 distance: 71 - 72: 15.476 distance: 71 - 74: 30.878 distance: 72 - 89: 30.661