Starting phenix.real_space_refine (version: dev) on Thu Dec 22 22:25:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/12_2022/6uqk_20849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/12_2022/6uqk_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_20849/12_2022/6uqk_20849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/12_2022/6uqk_20849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/12_2022/6uqk_20849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqk_20849/12_2022/6uqk_20849.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 29.06, per 1000 atoms: 0.56 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: 19.60 Conformation dependent library (CDL) restraints added in 8.1 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: 5.55 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: 29.22 Time building geometry restraints manager: 21.28 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 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. 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: 2.860 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: 0.060 Extract box with map and model: 13.670 Check model and map are aligned: 0.730 Convert atoms to be neutral: 0.440 Process input model: 144.540 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 % 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 *********************** 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 : 5.814 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 803 average time/residue: 0.5699 time to fit residues: 781.2535 Evaluate side-chains 510 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 6.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0484 ------------------------------------------------------------------------------- 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 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 ** A2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 226 GLN C 230 HIS C 245 HIS C 289 HIS C 391 HIS C 517 GLN C 571 GLN C 649 GLN C 783 HIS C 868 HIS ** C1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2120 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.084 52571 Z= 0.459 Angle : 0.663 7.948 72298 Z= 0.369 Chirality : 0.043 0.184 8595 Planarity : 0.005 0.097 9760 Dihedral : 4.336 28.136 8576 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 2.93 % 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: -0.55 (0.10), residues: 7856 helix: 1.06 (0.08), residues: 4720 sheet: -1.13 (0.24), residues: 484 loop : -2.95 (0.10), residues: 2652 *********************** 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: 78 poor density : 434 time to evaluate : 5.760 Fit side-chains outliers start: 78 outliers final: 42 residues processed: 496 average time/residue: 0.4821 time to fit residues: 437.4581 Evaluate side-chains 437 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 395 time to evaluate : 5.198 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4442 time to fit residues: 43.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 413 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 619 optimal weight: 0.0040 chunk 507 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 745 optimal weight: 20.0000 chunk 805 optimal weight: 10.0000 chunk 664 optimal weight: 0.0870 chunk 739 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 598 optimal weight: 2.9990 overall best weight: 1.9374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2119 ASN C 104 ASN C1249 HIS D1249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 52571 Z= 0.165 Angle : 0.457 8.462 72298 Z= 0.245 Chirality : 0.039 0.203 8595 Planarity : 0.003 0.087 9760 Dihedral : 3.634 28.354 8576 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.92 % 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: 0.44 (0.10), residues: 7856 helix: 1.90 (0.08), residues: 4712 sheet: -0.73 (0.25), residues: 484 loop : -2.64 (0.11), residues: 2660 *********************** 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 514 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 463 time to evaluate : 5.898 Fit side-chains outliers start: 51 outliers final: 25 residues processed: 501 average time/residue: 0.4971 time to fit residues: 452.5022 Evaluate side-chains 452 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 427 time to evaluate : 5.881 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4782 time to fit residues: 30.5905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 737 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 chunk 387 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 356 optimal weight: 5.9990 chunk 500 optimal weight: 10.0000 chunk 748 optimal weight: 9.9990 chunk 792 optimal weight: 0.9980 chunk 391 optimal weight: 0.9990 chunk 709 optimal weight: 30.0000 chunk 213 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS A1296 HIS B1296 HIS B2120 HIS C1296 HIS D1296 HIS D2120 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 52571 Z= 0.232 Angle : 0.503 10.691 72298 Z= 0.270 Chirality : 0.039 0.157 8595 Planarity : 0.004 0.097 9760 Dihedral : 3.761 28.868 8576 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 2.33 % 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: 0.76 (0.10), residues: 7856 helix: 2.16 (0.08), residues: 4704 sheet: -0.56 (0.25), residues: 484 loop : -2.52 (0.11), residues: 2668 *********************** 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 497 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 435 time to evaluate : 5.959 Fit side-chains outliers start: 62 outliers final: 22 residues processed: 482 average time/residue: 0.4994 time to fit residues: 444.2640 Evaluate side-chains 432 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 410 time to evaluate : 5.717 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4499 time to fit residues: 26.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 590 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 676 optimal weight: 8.9990 chunk 547 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 711 optimal weight: 40.0000 chunk 200 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN C 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 52571 Z= 0.462 Angle : 0.678 9.488 72298 Z= 0.373 Chirality : 0.044 0.207 8595 Planarity : 0.005 0.098 9760 Dihedral : 4.649 29.404 8576 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer Outliers : 2.71 % 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: 0.14 (0.10), residues: 7856 helix: 1.59 (0.08), residues: 4748 sheet: -0.59 (0.26), residues: 476 loop : -2.72 (0.11), residues: 2632 *********************** 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 468 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 396 time to evaluate : 4.915 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 42 residues processed: 451 average time/residue: 0.4863 time to fit residues: 405.5163 Evaluate side-chains 424 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 382 time to evaluate : 6.019 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4666 time to fit residues: 44.6132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 266 optimal weight: 6.9990 chunk 713 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 793 optimal weight: 10.0000 chunk 658 optimal weight: 2.9990 chunk 367 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 416 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN D 783 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 52571 Z= 0.214 Angle : 0.496 8.703 72298 Z= 0.267 Chirality : 0.039 0.150 8595 Planarity : 0.003 0.097 9760 Dihedral : 3.960 28.850 8576 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7856 helix: 2.16 (0.08), residues: 4724 sheet: -0.74 (0.25), residues: 484 loop : -2.53 (0.11), residues: 2648 *********************** 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 462 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 426 time to evaluate : 6.296 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 447 average time/residue: 0.4828 time to fit residues: 398.1903 Evaluate side-chains 419 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 403 time to evaluate : 5.751 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4437 time to fit residues: 20.7999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 764 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 579 optimal weight: 1.9990 chunk 448 optimal weight: 7.9990 chunk 667 optimal weight: 9.9990 chunk 443 optimal weight: 10.0000 chunk 790 optimal weight: 20.0000 chunk 494 optimal weight: 10.0000 chunk 481 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 D 126 HIS D 783 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.074 52571 Z= 0.541 Angle : 0.734 10.277 72298 Z= 0.406 Chirality : 0.045 0.166 8595 Planarity : 0.005 0.101 9760 Dihedral : 4.913 29.602 8576 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.51 % Favored : 90.44 % Rotamer Outliers : 2.26 % 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: -0.14 (0.10), residues: 7856 helix: 1.42 (0.08), residues: 4700 sheet: -1.28 (0.23), residues: 548 loop : -2.77 (0.11), residues: 2608 *********************** 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 438 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 378 time to evaluate : 5.283 Fit side-chains outliers start: 60 outliers final: 32 residues processed: 420 average time/residue: 0.4796 time to fit residues: 372.3718 Evaluate side-chains 401 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 369 time to evaluate : 5.279 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4253 time to fit residues: 33.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 488 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 472 optimal weight: 0.3980 chunk 238 optimal weight: 2.9990 chunk 155 optimal weight: 50.0000 chunk 153 optimal weight: 4.9990 chunk 502 optimal weight: 0.0370 chunk 538 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 621 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 783 HIS C2510 ASN D 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 52571 Z= 0.138 Angle : 0.479 10.207 72298 Z= 0.254 Chirality : 0.039 0.153 8595 Planarity : 0.003 0.095 9760 Dihedral : 3.870 27.889 8576 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 7856 helix: 2.25 (0.08), residues: 4728 sheet: -0.91 (0.25), residues: 484 loop : -2.43 (0.11), residues: 2644 *********************** REFINEMENT MACRO_CYCLE 8 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 462 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 450 time to evaluate : 5.296 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 456 average time/residue: 0.4741 time to fit residues: 400.0894 Evaluate side-chains 429 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 419 time to evaluate : 6.016 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3728 time to fit residues: 13.6543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 718 optimal weight: 7.9990 chunk 757 optimal weight: 5.9990 chunk 690 optimal weight: 10.0000 chunk 736 optimal weight: 10.0000 chunk 756 optimal weight: 1.9990 chunk 443 optimal weight: 9.9990 chunk 320 optimal weight: 0.0040 chunk 578 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 665 optimal weight: 0.8980 chunk 696 optimal weight: 0.9980 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 HIS A2468 HIS B 783 HIS C 783 HIS D 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 52571 Z= 0.176 Angle : 0.482 9.593 72298 Z= 0.255 Chirality : 0.039 0.164 8595 Planarity : 0.003 0.099 9760 Dihedral : 3.712 27.721 8576 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.49 % 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: 1.06 (0.10), residues: 7856 helix: 2.37 (0.08), residues: 4764 sheet: -0.87 (0.25), residues: 488 loop : -2.33 (0.12), residues: 2604 *********************** REFINEMENT MACRO_CYCLE 9 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 434 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 421 time to evaluate : 5.225 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 428 average time/residue: 0.4796 time to fit residues: 381.0264 Evaluate side-chains 422 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 415 time to evaluate : 5.602 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4422 time to fit residues: 13.3595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 733 optimal weight: 30.0000 chunk 483 optimal weight: 10.0000 chunk 778 optimal weight: 7.9990 chunk 475 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 541 optimal weight: 2.9990 chunk 816 optimal weight: 0.0020 chunk 751 optimal weight: 9.9990 chunk 650 optimal weight: 10.0000 chunk 67 optimal weight: 0.0000 chunk 502 optimal weight: 9.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 783 HIS C2472 ASN D 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 52571 Z= 0.182 Angle : 0.480 9.473 72298 Z= 0.254 Chirality : 0.039 0.165 8595 Planarity : 0.003 0.100 9760 Dihedral : 3.647 26.497 8576 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.38 % 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: 1.17 (0.10), residues: 7856 helix: 2.46 (0.08), residues: 4768 sheet: -0.85 (0.25), residues: 488 loop : -2.31 (0.12), residues: 2600 ********************** REFINEMENT MACRO_CYCLE 10 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 430 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 420 time to evaluate : 4.996 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 427 average time/residue: 0.4557 time to fit residues: 360.9438 Evaluate side-chains 422 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 414 time to evaluate : 4.778 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4250 time to fit residues: 13.3172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 820 random chunks: chunk 398 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 chunk 692 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 599 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 180 optimal weight: 7.9990 chunk 651 optimal weight: 0.0370 chunk 272 optimal weight: 0.0970 chunk 669 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 overall best weight: 2.8260 ------------------------------------------------------------------------------- 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 783 HIS C2472 ASN D 783 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.071431 restraints weight = 180026.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073409 restraints weight = 87665.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074750 restraints weight = 54261.427| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4476 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= 0.217 Angle : 0.500 9.222 72298 Z= 0.266 Chirality : 0.039 0.147 8595 Planarity : 0.003 0.099 9760 Dihedral : 3.736 25.692 8576 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.30 % 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: 1.15 (0.10), residues: 7856 helix: 2.44 (0.08), residues: 4772 sheet: -0.81 (0.25), residues: 480 loop : -2.30 (0.12), residues: 2604 =============================================================================== Job complete usr+sys time: 8753.63 seconds wall clock time: 155 minutes 42.89 seconds (9342.89 seconds total)