Starting phenix.real_space_refine on Thu Dec 14 10:51:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bk8_7109/12_2023/6bk8_7109_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 442 5.49 5 Mg 5 5.21 5 S 240 5.16 5 C 50496 2.51 5 N 14743 2.21 5 O 16812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1212": "NH1" <-> "NH2" Residue "A ARG 1217": "NH1" <-> "NH2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1315": "NH1" <-> "NH2" Residue "A ARG 1347": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1486": "NH1" <-> "NH2" Residue "A ARG 1490": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A ARG 1512": "NH1" <-> "NH2" Residue "A ARG 1521": "NH1" <-> "NH2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A ARG 1595": "NH1" <-> "NH2" Residue "A ARG 1616": "NH1" <-> "NH2" Residue "A ARG 1904": "NH1" <-> "NH2" Residue "A ARG 1998": "NH1" <-> "NH2" Residue "A ARG 2056": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 973": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 215": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "H ARG 29": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ARG 81": "NH1" <-> "NH2" Residue "L ARG 382": "NH1" <-> "NH2" Residue "L ARG 439": "NH1" <-> "NH2" Residue "L ARG 459": "NH1" <-> "NH2" Residue "M ARG 58": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N ARG 215": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "O ARG 191": "NH1" <-> "NH2" Residue "O ARG 243": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 290": "NH1" <-> "NH2" Residue "P ARG 988": "NH1" <-> "NH2" Residue "P PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 1036": "NH1" <-> "NH2" Residue "P ARG 1134": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 93": "NH1" <-> "NH2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ARG 138": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 172": "NH1" <-> "NH2" Residue "S ARG 189": "NH1" <-> "NH2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ARG 246": "NH1" <-> "NH2" Residue "S ARG 250": "NH1" <-> "NH2" Residue "T ARG 44": "NH1" <-> "NH2" Residue "T ARG 51": "NH1" <-> "NH2" Residue "T ARG 131": "NH1" <-> "NH2" Residue "T ARG 186": "NH1" <-> "NH2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 211": "NH1" <-> "NH2" Residue "U ARG 726": "NH1" <-> "NH2" Residue "U ARG 760": "NH1" <-> "NH2" Residue "U ARG 776": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ARG 97": "NH1" <-> "NH2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "n TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 30": "NH1" <-> "NH2" Residue "p GLU 13": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 82745 Number of models: 1 Model: "" Number of chains: 53 Chain: "2" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2848 Classifications: {'RNA': 135} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 13, 'rna3p_pur': 56, 'rna3p_pyr': 65} Link IDs: {'rna2p': 14, 'rna3p': 120} Chain breaks: 7 Chain: "5" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2173 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 35, 'rna3p_pyr': 49} Link IDs: {'rna2p': 18, 'rna3p': 84} Chain breaks: 2 Chain: "6" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2170 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 45, 'rna3p_pyr': 35} Link IDs: {'rna2p': 22, 'rna3p': 79} Chain: "e" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 707 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 17} Link IDs: {'rna2p': 10, 'rna3p': 23} Chain: "i" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1239 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 9, 'rna3p_pur': 23, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 45} Chain breaks: 4 Chain: "A" Number of atoms: 16159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1960, 16159 Classifications: {'peptide': 1960} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 101, 'TRANS': 1856} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7179 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 49, 'TRANS': 848} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2826 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 345} Chain: "E" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1494 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 12, 'TRANS': 173} Chain breaks: 4 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2048 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 570 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1283 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "K" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 550 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "L" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3353 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 405} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2607 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1326 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "O" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1935 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 3872 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 30, 'TRANS': 622} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1382 Unresolved non-hydrogen angles: 1758 Unresolved non-hydrogen dihedrals: 1119 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 4, 'TYR:plan': 18, 'ASN:plan1': 22, 'TRP:plan': 1, 'ASP:plan': 27, 'PHE:plan': 13, 'GLU:plan': 32, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 716 Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 813 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'TRANS': 100} Chain breaks: 1 Chain: "S" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1948 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain breaks: 1 Chain: "T" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3370 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 8, 'TRANS': 474} Chain breaks: 15 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 840 Unresolved non-hydrogen angles: 1080 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 17, 'ASN:plan1': 5, 'TRP:plan': 8, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 503 Chain: "U" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 3625 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 457} Link IDs: {'PTRANS': 18, 'TRANS': 618} Chain breaks: 24 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1821 Unresolved non-hydrogen angles: 2350 Unresolved non-hydrogen dihedrals: 1571 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 7, 'TYR:plan': 30, 'ASN:plan1': 20, 'TRP:plan': 17, 'ASP:plan': 27, 'PHE:plan': 22, 'GLU:plan': 51, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 1085 Chain: "X" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1095 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'TRANS': 218} Chain breaks: 4 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 219 Planarities with less than four sites: {'UNK:plan-1': 219} Unresolved non-hydrogen planarities: 219 Chain: "Y" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "a" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "b" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 631 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "k" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "l" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "p" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 618 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "q" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "r" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "s" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 816 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 294 Chain: "u" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2156 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 392} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1365 Unresolved non-hydrogen angles: 1753 Unresolved non-hydrogen dihedrals: 1136 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 700 Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 588 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "w" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2171 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1372 Unresolved non-hydrogen angles: 1761 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 5, 'TYR:plan': 21, 'ASN:plan1': 25, 'TRP:plan': 6, 'ASP:plan': 35, 'PHE:plan': 12, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 708 Chain: "x" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 578 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 155 Chain: "y" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 548 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" 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 36877 SG CYS F 13 100.518 194.427 148.794 1.00 34.08 S ATOM 36901 SG CYS F 16 99.283 191.178 151.106 1.00 30.71 S ATOM 37335 SG CYS F 71 102.650 190.253 149.649 1.00 21.82 S ATOM 37356 SG CYS F 74 99.161 190.552 149.885 1.00 26.26 S ATOM 37035 SG CYS F 34 107.824 178.974 146.475 1.00 17.23 S ATOM 37058 SG CYS F 37 111.785 177.475 145.272 1.00 17.38 S ATOM 37257 SG CYS F 61 112.214 180.371 147.963 1.00 18.49 S ATOM 37281 SG CYS F 64 110.068 180.386 144.070 1.00 17.06 S ATOM 38938 SG CYS G 73 80.144 175.298 157.436 1.00 19.75 S ATOM 39000 SG CYS G 81 77.629 173.868 159.362 1.00 25.00 S ATOM 39040 SG CYS G 87 79.954 176.701 160.814 1.00 28.08 S ATOM 41869 SG CYS I 104 89.742 179.011 184.002 1.00 21.41 S ATOM 41875 SG CYS I 105 91.261 176.391 183.491 1.00 20.17 S ATOM 41900 SG CYS I 108 92.138 179.577 181.469 1.00 22.54 S ATOM 42214 SG CYS I 148 90.133 176.356 182.470 1.00 22.99 S ATOM 41869 SG CYS I 104 89.742 179.011 184.002 1.00 21.41 S ATOM 42003 SG CYS I 122 89.764 182.254 181.659 1.00 18.81 S ATOM 42224 SG CYS I 150 86.506 181.110 182.790 1.00 22.85 S ATOM 42245 SG CYS I 153 88.563 182.733 184.334 1.00 21.37 S ATOM 41900 SG CYS I 108 92.138 179.577 181.469 1.00 22.54 S ATOM 41989 SG CYS I 120 92.172 181.670 178.601 1.00 18.59 S ATOM 42003 SG CYS I 122 89.764 182.254 181.659 1.00 18.81 S ATOM 42191 SG CYS I 145 90.403 179.612 178.063 1.00 19.91 S ATOM 50519 SG CYS O 122 117.240 127.822 216.287 1.00 67.70 S ATOM 50538 SG CYS O 125 114.171 129.425 214.703 1.00 61.11 S ATOM 50611 SG CYS O 135 114.619 130.403 213.971 1.00 49.27 S Time building chain proxies: 32.26, per 1000 atoms: 0.39 Number of scatterers: 82745 At special positions: 0 Unit cell: (244.8, 288.32, 297.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 240 16.00 P 442 15.00 Mg 5 11.99 O 16812 8.00 N 14743 7.00 C 50496 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: 26.60 Conformation dependent library (CDL) restraints added in 10.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 74 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 13 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 64 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 34 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 61 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 91 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 81 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 87 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 73 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 148 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 105 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 104 " pdb=" ZN I 502 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 153 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 104 " pdb="ZN ZN I 502 " - pdb=" SG CYS I 122 " pdb=" ZN I 503 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 120 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 108 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 145 " pdb="ZN ZN I 503 " - pdb=" SG CYS I 122 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" NE2 HIS O 130 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 125 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 122 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 135 " Number of angles added : 36 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 93 sheets defined 41.2% alpha, 11.7% beta 111 base pairs and 221 stacking pairs defined. Time for finding SS restraints: 27.08 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.889A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 4.156A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.306A pdb=" N LYS A 474 " --> pdb=" O PRO A 471 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 475 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 516 through 534 removed outlier: 3.613A pdb=" N GLN A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 No H-bonds generated for 'chain 'A' and resid 548 through 551' Processing helix chain 'A' and resid 564 through 585 removed outlier: 3.707A pdb=" N LEU A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 671 through 691 removed outlier: 3.977A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 689 " --> pdb=" O ILE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 735 removed outlier: 3.781A pdb=" N GLY A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 767 removed outlier: 4.013A pdb=" N ASP A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 794 removed outlier: 4.065A pdb=" N ARG A 780 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 783 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 784 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 788 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 842 through 870 removed outlier: 3.653A pdb=" N ARG A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 908 through 924 removed outlier: 3.887A pdb=" N ASP A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 924 " --> pdb=" O LYS A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 947 through 960 removed outlier: 3.782A pdb=" N LEU A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1005 removed outlier: 3.643A pdb=" N ILE A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1063 through 1070 Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1108 through 1126 removed outlier: 4.488A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A1112 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A1117 " --> pdb=" O PHE A1114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1126 " --> pdb=" O LEU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1272 through 1274 No H-bonds generated for 'chain 'A' and resid 1272 through 1274' Processing helix chain 'A' and resid 1306 through 1322 removed outlier: 3.574A pdb=" N LEU A1320 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.841A pdb=" N LEU A1342 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1350 No H-bonds generated for 'chain 'A' and resid 1348 through 1350' Processing helix chain 'A' and resid 1354 through 1374 Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1471 removed outlier: 3.668A pdb=" N ARG A1456 " --> pdb=" O LEU A1452 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A1470 " --> pdb=" O GLN A1466 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A1471 " --> pdb=" O GLU A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.853A pdb=" N LYS A1515 " --> pdb=" O ARG A1511 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1541 through 1549 removed outlier: 3.890A pdb=" N ILE A1547 " --> pdb=" O ARG A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1557 Processing helix chain 'A' and resid 1562 through 1565 No H-bonds generated for 'chain 'A' and resid 1562 through 1565' Processing helix chain 'A' and resid 1570 through 1573 Processing helix chain 'A' and resid 1581 through 1587 removed outlier: 4.434A pdb=" N PHE A1587 " --> pdb=" O ASP A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1595 No H-bonds generated for 'chain 'A' and resid 1592 through 1595' Processing helix chain 'A' and resid 1598 through 1609 Proline residue: A1602 - end of helix removed outlier: 3.500A pdb=" N PHE A1606 " --> pdb=" O ASN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 3.589A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1670 Processing helix chain 'A' and resid 1690 through 1692 No H-bonds generated for 'chain 'A' and resid 1690 through 1692' Processing helix chain 'A' and resid 1748 through 1759 Processing helix chain 'A' and resid 1794 through 1808 Processing helix chain 'A' and resid 1810 through 1823 Processing helix chain 'A' and resid 1840 through 1844 removed outlier: 3.741A pdb=" N LEU A1843 " --> pdb=" O TYR A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1899 Processing helix chain 'A' and resid 1908 through 1923 Processing helix chain 'A' and resid 1938 through 1949 removed outlier: 4.564A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix Processing helix chain 'A' and resid 1965 through 1970 Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 1995 through 1998 No H-bonds generated for 'chain 'A' and resid 1995 through 1998' Processing helix chain 'A' and resid 2001 through 2017 Processing helix chain 'A' and resid 2021 through 2026 Processing helix chain 'A' and resid 2045 through 2067 Processing helix chain 'A' and resid 2076 through 2083 Processing helix chain 'A' and resid 2091 through 2105 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.749A pdb=" N ALA B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.638A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.795A pdb=" N ILE B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 274' Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.821A pdb=" N SER B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.548A pdb=" N TYR B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 347 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.774A pdb=" N ASN B 398 " --> pdb=" O ASP B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 445 through 456 removed outlier: 5.203A pdb=" N ASP B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 515 removed outlier: 4.403A pdb=" N GLU B 508 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN B 511 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 612 through 628 Proline residue: B 616 - end of helix removed outlier: 4.386A pdb=" N ASP B 620 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 717 through 723 removed outlier: 4.026A pdb=" N GLN B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.663A pdb=" N ILE B 750 " --> pdb=" O LYS B 746 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 792 through 804 Processing helix chain 'B' and resid 832 through 852 Proline residue: B 840 - end of helix removed outlier: 4.081A pdb=" N LYS B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 844 " --> pdb=" O PRO B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 882 removed outlier: 3.678A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 921 removed outlier: 3.672A pdb=" N ARG B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 973 Processing helix chain 'B' and resid 989 through 991 No H-bonds generated for 'chain 'B' and resid 989 through 991' Processing helix chain 'B' and resid 995 through 1003 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.677A pdb=" N ILE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 111 through 119 removed outlier: 4.104A pdb=" N LEU D 118 " --> pdb=" O ARG D 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 119 " --> pdb=" O TYR D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 60 through 83 removed outlier: 3.787A pdb=" N GLN E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 182 through 185 No H-bonds generated for 'chain 'E' and resid 182 through 185' Processing helix chain 'E' and resid 199 through 227 Processing helix chain 'F' and resid 14 through 17 No H-bonds generated for 'chain 'F' and resid 14 through 17' Processing helix chain 'F' and resid 62 through 67 Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.554A pdb=" N HIS F 89 " --> pdb=" O GLN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.578A pdb=" N ARG F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 4.005A pdb=" N GLN F 124 " --> pdb=" O GLY F 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE F 125 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR F 126 " --> pdb=" O ALA F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 121 through 126' Processing helix chain 'F' and resid 129 through 146 removed outlier: 3.681A pdb=" N VAL F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'G' and resid 63 through 66 No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 96 through 104 removed outlier: 3.507A pdb=" N LYS G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 145 No H-bonds generated for 'chain 'G' and resid 142 through 145' Processing helix chain 'G' and resid 154 through 166 removed outlier: 4.136A pdb=" N ARG G 166 " --> pdb=" O PHE G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 198 Processing helix chain 'G' and resid 232 through 255 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 165 through 173 Processing helix chain 'I' and resid 14 through 33 removed outlier: 3.885A pdb=" N GLU I 17 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS I 20 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Proline residue: I 21 - end of helix Processing helix chain 'I' and resid 43 through 67 removed outlier: 4.183A pdb=" N GLN I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 83 removed outlier: 3.717A pdb=" N TRP I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 95 Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 121 through 123 No H-bonds generated for 'chain 'I' and resid 121 through 123' Processing helix chain 'I' and resid 126 through 136 Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 59 through 86 Processing helix chain 'K' and resid 92 through 114 Processing helix chain 'L' and resid 15 through 30 Proline residue: L 27 - end of helix removed outlier: 3.968A pdb=" N SER L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 44 Processing helix chain 'L' and resid 53 through 64 Processing helix chain 'L' and resid 72 through 86 Processing helix chain 'L' and resid 88 through 107 Processing helix chain 'L' and resid 111 through 127 removed outlier: 3.693A pdb=" N TYR L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 143 Processing helix chain 'L' and resid 151 through 165 removed outlier: 3.843A pdb=" N MET L 155 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TRP L 160 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS L 161 " --> pdb=" O ILE L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 182 Processing helix chain 'L' and resid 188 through 201 Processing helix chain 'L' and resid 250 through 261 removed outlier: 3.582A pdb=" N ALA L 254 " --> pdb=" O GLU L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 300 Processing helix chain 'L' and resid 305 through 315 Processing helix chain 'L' and resid 322 through 333 Processing helix chain 'L' and resid 342 through 351 removed outlier: 3.852A pdb=" N SER L 347 " --> pdb=" O TYR L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 370 removed outlier: 4.073A pdb=" N GLU L 366 " --> pdb=" O ASN L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 375 removed outlier: 3.616A pdb=" N ASP L 375 " --> pdb=" O ASP L 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 372 through 375' Processing helix chain 'L' and resid 378 through 393 removed outlier: 3.787A pdb=" N ILE L 383 " --> pdb=" O ASP L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 404 removed outlier: 3.936A pdb=" N ILE L 404 " --> pdb=" O CYS L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 430 removed outlier: 3.605A pdb=" N PHE L 419 " --> pdb=" O GLN L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 443 Processing helix chain 'L' and resid 455 through 468 Processing helix chain 'L' and resid 472 through 485 removed outlier: 4.128A pdb=" N GLU L 475 " --> pdb=" O LEU L 472 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP L 476 " --> pdb=" O LEU L 473 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 61 removed outlier: 3.713A pdb=" N LYS M 57 " --> pdb=" O LYS M 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 88 Processing helix chain 'N' and resid 97 through 99 No H-bonds generated for 'chain 'N' and resid 97 through 99' Processing helix chain 'N' and resid 107 through 127 removed outlier: 3.854A pdb=" N SER N 127 " --> pdb=" O ARG N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 151 Proline residue: N 145 - end of helix Processing helix chain 'N' and resid 157 through 171 removed outlier: 3.591A pdb=" N SER N 162 " --> pdb=" O ASP N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 187 removed outlier: 3.637A pdb=" N VAL N 180 " --> pdb=" O ILE N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 210 Processing helix chain 'N' and resid 219 through 221 No H-bonds generated for 'chain 'N' and resid 219 through 221' Processing helix chain 'N' and resid 224 through 246 Processing helix chain 'O' and resid 35 through 38 No H-bonds generated for 'chain 'O' and resid 35 through 38' Processing helix chain 'O' and resid 42 through 44 No H-bonds generated for 'chain 'O' and resid 42 through 44' Processing helix chain 'O' and resid 132 through 134 No H-bonds generated for 'chain 'O' and resid 132 through 134' Processing helix chain 'O' and resid 167 through 170 No H-bonds generated for 'chain 'O' and resid 167 through 170' Processing helix chain 'O' and resid 180 through 196 Processing helix chain 'O' and resid 216 through 224 Processing helix chain 'O' and resid 294 through 313 removed outlier: 4.012A pdb=" N LEU O 302 " --> pdb=" O LYS O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 346 Processing helix chain 'P' and resid 477 through 480 No H-bonds generated for 'chain 'P' and resid 477 through 480' Processing helix chain 'P' and resid 485 through 495 removed outlier: 6.466A pdb=" N SER P 490 " --> pdb=" O ALA P 487 " (cutoff:3.500A) Processing helix chain 'P' and resid 512 through 524 removed outlier: 4.218A pdb=" N THR P 517 " --> pdb=" O THR P 513 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN P 518 " --> pdb=" O THR P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 538 through 552 Processing helix chain 'P' and resid 581 through 590 Processing helix chain 'P' and resid 610 through 625 removed outlier: 4.002A pdb=" N LYS P 621 " --> pdb=" O ALA P 617 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE P 624 " --> pdb=" O LYS P 620 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS P 625 " --> pdb=" O LYS P 621 " (cutoff:3.500A) Processing helix chain 'P' and resid 641 through 646 Processing helix chain 'P' and resid 674 through 687 Processing helix chain 'P' and resid 701 through 717 Processing helix chain 'P' and resid 736 through 743 removed outlier: 3.872A pdb=" N LYS P 741 " --> pdb=" O GLU P 737 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE P 742 " --> pdb=" O ILE P 738 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE P 743 " --> pdb=" O GLN P 739 " (cutoff:3.500A) Processing helix chain 'P' and resid 758 through 762 removed outlier: 4.070A pdb=" N THR P 762 " --> pdb=" O ILE P 759 " (cutoff:3.500A) Processing helix chain 'P' and resid 799 through 810 removed outlier: 3.826A pdb=" N ALA P 809 " --> pdb=" O ARG P 805 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY P 810 " --> pdb=" O LYS P 806 " (cutoff:3.500A) Processing helix chain 'P' and resid 823 through 828 Processing helix chain 'P' and resid 846 through 853 Processing helix chain 'P' and resid 869 through 881 Processing helix chain 'P' and resid 893 through 899 Processing helix chain 'P' and resid 905 through 916 Processing helix chain 'P' and resid 920 through 931 Processing helix chain 'P' and resid 943 through 953 Processing helix chain 'P' and resid 960 through 972 removed outlier: 3.563A pdb=" N LEU P 964 " --> pdb=" O HIS P 960 " (cutoff:3.500A) Processing helix chain 'P' and resid 977 through 982 Processing helix chain 'P' and resid 987 through 1005 Processing helix chain 'P' and resid 1018 through 1029 removed outlier: 3.712A pdb=" N GLY P1028 " --> pdb=" O THR P1024 " (cutoff:3.500A) Processing helix chain 'P' and resid 1088 through 1094 Processing helix chain 'P' and resid 1130 through 1140 Processing helix chain 'R' and resid 97 through 117 removed outlier: 3.979A pdb=" N LYS R 102 " --> pdb=" O ASP R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 188 Processing helix chain 'R' and resid 198 through 214 removed outlier: 4.054A pdb=" N GLN R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY R 213 " --> pdb=" O ARG R 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 28 removed outlier: 4.085A pdb=" N LYS S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 37 No H-bonds generated for 'chain 'S' and resid 34 through 37' Processing helix chain 'S' and resid 45 through 54 Processing helix chain 'S' and resid 67 through 79 Processing helix chain 'S' and resid 84 through 91 Processing helix chain 'S' and resid 95 through 107 Processing helix chain 'S' and resid 132 through 134 No H-bonds generated for 'chain 'S' and resid 132 through 134' Processing helix chain 'S' and resid 146 through 160 Processing helix chain 'S' and resid 165 through 194 removed outlier: 3.681A pdb=" N ARG S 188 " --> pdb=" O GLU S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 250 Processing helix chain 'T' and resid 15 through 27 Processing helix chain 'T' and resid 40 through 60 Processing helix chain 'T' and resid 65 through 77 Processing helix chain 'T' and resid 81 through 94 removed outlier: 3.697A pdb=" N VAL T 94 " --> pdb=" O ARG T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 112 removed outlier: 4.327A pdb=" N VAL T 112 " --> pdb=" O ALA T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 128 Processing helix chain 'T' and resid 133 through 145 Processing helix chain 'T' and resid 149 through 161 Processing helix chain 'T' and resid 166 through 178 Processing helix chain 'T' and resid 182 through 195 removed outlier: 4.100A pdb=" N ARG T 186 " --> pdb=" O TRP T 182 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU T 187 " --> pdb=" O ASN T 183 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET T 194 " --> pdb=" O SER T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 212 Processing helix chain 'T' and resid 215 through 234 removed outlier: 3.740A pdb=" N THR T 228 " --> pdb=" O LEU T 224 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN T 233 " --> pdb=" O VAL T 229 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASN T 234 " --> pdb=" O ALA T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 240 through 256 Processing helix chain 'T' and resid 260 through 273 Processing helix chain 'T' and resid 278 through 290 Processing helix chain 'T' and resid 296 through 314 Processing helix chain 'T' and resid 321 through 331 Processing helix chain 'T' and resid 335 through 348 Processing helix chain 'T' and resid 357 through 375 Processing helix chain 'T' and resid 383 through 394 Processing helix chain 'T' and resid 404 through 415 Processing helix chain 'T' and resid 420 through 429 Processing helix chain 'T' and resid 441 through 449 Processing helix chain 'T' and resid 453 through 466 Processing helix chain 'T' and resid 471 through 482 Processing helix chain 'T' and resid 488 through 499 Processing helix chain 'T' and resid 508 through 520 Processing helix chain 'T' and resid 532 through 539 Processing helix chain 'T' and resid 546 through 555 Processing helix chain 'U' and resid 22 through 32 Processing helix chain 'U' and resid 38 through 47 removed outlier: 3.624A pdb=" N TYR U 46 " --> pdb=" O ARG U 42 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP U 47 " --> pdb=" O TYR U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 67 Processing helix chain 'U' and resid 72 through 82 Processing helix chain 'U' and resid 90 through 101 Processing helix chain 'U' and resid 108 through 119 Processing helix chain 'U' and resid 128 through 138 Processing helix chain 'U' and resid 146 through 158 Proline residue: U 150 - end of helix Processing helix chain 'U' and resid 175 through 190 Processing helix chain 'U' and resid 210 through 217 Processing helix chain 'U' and resid 225 through 235 Processing helix chain 'U' and resid 242 through 250 Processing helix chain 'U' and resid 271 through 281 Processing helix chain 'U' and resid 285 through 295 Processing helix chain 'U' and resid 301 through 312 Processing helix chain 'U' and resid 318 through 331 Processing helix chain 'U' and resid 340 through 364 removed outlier: 3.540A pdb=" N LYS U 362 " --> pdb=" O LEU U 358 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU U 363 " --> pdb=" O GLY U 359 " (cutoff:3.500A) Processing helix chain 'U' and resid 374 through 401 removed outlier: 3.720A pdb=" N TYR U 392 " --> pdb=" O LEU U 388 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP U 393 " --> pdb=" O ILE U 389 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE U 394 " --> pdb=" O ASN U 390 " (cutoff:3.500A) Processing helix chain 'U' and resid 408 through 417 Processing helix chain 'U' and resid 425 through 434 Processing helix chain 'U' and resid 436 through 439 No H-bonds generated for 'chain 'U' and resid 436 through 439' Processing helix chain 'U' and resid 450 through 460 Processing helix chain 'U' and resid 463 through 474 Processing helix chain 'U' and resid 484 through 496 Processing helix chain 'U' and resid 502 through 522 Proline residue: U 515 - end of helix Proline residue: U 518 - end of helix Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'U' and resid 568 through 579 Processing helix chain 'U' and resid 586 through 596 Processing helix chain 'U' and resid 602 through 612 Processing helix chain 'U' and resid 619 through 633 Processing helix chain 'U' and resid 642 through 655 Processing helix chain 'U' and resid 664 through 674 Processing helix chain 'U' and resid 683 through 692 Processing helix chain 'U' and resid 703 through 718 Processing helix chain 'U' and resid 724 through 734 Processing helix chain 'U' and resid 738 through 755 removed outlier: 4.303A pdb=" N GLU U 743 " --> pdb=" O SER U 739 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE U 755 " --> pdb=" O PHE U 751 " (cutoff:3.500A) Processing helix chain 'U' and resid 761 through 770 Processing helix chain 'U' and resid 778 through 791 Processing helix chain 'U' and resid 794 through 807 Processing helix chain 'X' and resid 29 through 50 removed outlier: 3.592A pdb=" N UNK X 49 " --> pdb=" O UNK X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 79 removed outlier: 3.743A pdb=" N UNK X 74 " --> pdb=" O UNK X 70 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N UNK X 78 " --> pdb=" O UNK X 74 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N UNK X 79 " --> pdb=" O UNK X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 124 removed outlier: 3.956A pdb=" N UNK X 117 " --> pdb=" O UNK X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 1007 through 1023 removed outlier: 4.041A pdb=" N UNK X1012 " --> pdb=" O UNK X1008 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N UNK X1013 " --> pdb=" O UNK X1009 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N UNK X1023 " --> pdb=" O UNK X1019 " (cutoff:3.500A) Processing helix chain 'X' and resid 2293 through 2304 removed outlier: 3.772A pdb=" N UNK X2298 " --> pdb=" O UNK X2294 " (cutoff:3.500A) Processing helix chain 'X' and resid 2310 through 2312 No H-bonds generated for 'chain 'X' and resid 2310 through 2312' Processing helix chain 'X' and resid 2314 through 2318 Processing helix chain 'X' and resid 3395 through 3402 removed outlier: 3.665A pdb=" N UNK X3402 " --> pdb=" O UNK X3398 " (cutoff:3.500A) Processing helix chain 'X' and resid 3406 through 3430 Processing helix chain 'Y' and resid 2 through 15 Processing helix chain 'a' and resid 16 through 28 Processing helix chain 'a' and resid 30 through 40 removed outlier: 3.993A pdb=" N ILE a 34 " --> pdb=" O MET a 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA a 37 " --> pdb=" O ILE a 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR a 40 " --> pdb=" O ALA a 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 22 Processing helix chain 'c' and resid 13 through 23 Processing helix chain 'c' and resid 84 through 86 No H-bonds generated for 'chain 'c' and resid 84 through 86' Processing helix chain 'f' and resid 13 through 15 No H-bonds generated for 'chain 'f' and resid 13 through 15' Processing helix chain 'g' and resid 6 through 13 Processing helix chain 'g' and resid 66 through 68 No H-bonds generated for 'chain 'g' and resid 66 through 68' Processing helix chain 'h' and resid 3 through 9 Processing helix chain 'h' and resid 103 through 107 Processing helix chain 'l' and resid 13 through 23 removed outlier: 3.586A pdb=" N ILE l 17 " --> pdb=" O PRO l 13 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE l 18 " --> pdb=" O ILE l 14 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 21 Processing helix chain 'o' and resid 6 through 13 Processing helix chain 'p' and resid 4 through 9 Processing helix chain 'q' and resid 17 through 20 No H-bonds generated for 'chain 'q' and resid 17 through 20' Processing helix chain 'q' and resid 25 through 28 No H-bonds generated for 'chain 'q' and resid 25 through 28' Processing helix chain 'q' and resid 32 through 39 Processing helix chain 'r' and resid 41 through 52 Processing helix chain 'r' and resid 79 through 88 Processing helix chain 's' and resid 5 through 10 Processing helix chain 's' and resid 43 through 45 No H-bonds generated for 'chain 's' and resid 43 through 45' Processing helix chain 's' and resid 112 through 115 Processing helix chain 's' and resid 140 through 147 Processing helix chain 's' and resid 161 through 166 Processing helix chain 'u' and resid 25 through 34 removed outlier: 3.562A pdb=" N GLN u 30 " --> pdb=" O SER u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 78 through 105 removed outlier: 3.815A pdb=" N LEU u 93 " --> pdb=" O ASP u 89 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU u 98 " --> pdb=" O GLU u 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR u 101 " --> pdb=" O LYS u 97 " (cutoff:3.500A) Processing helix chain 'u' and resid 107 through 136 removed outlier: 3.780A pdb=" N THR u 111 " --> pdb=" O LYS u 107 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL u 112 " --> pdb=" O LYS u 108 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL u 122 " --> pdb=" O ALA u 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN u 131 " --> pdb=" O LEU u 127 " (cutoff:3.500A) Processing helix chain 'v' and resid 25 through 34 removed outlier: 3.578A pdb=" N LYS v 33 " --> pdb=" O GLU v 29 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 80 No H-bonds generated for 'chain 'v' and resid 77 through 80' Processing helix chain 'v' and resid 82 through 140 removed outlier: 3.502A pdb=" N LEU v 105 " --> pdb=" O THR v 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER v 110 " --> pdb=" O THR v 106 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR v 111 " --> pdb=" O LYS v 107 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU v 132 " --> pdb=" O MET v 128 " (cutoff:3.500A) Proline residue: v 138 - end of helix Processing helix chain 'w' and resid 25 through 34 Processing helix chain 'w' and resid 79 through 142 removed outlier: 3.562A pdb=" N ALA w 90 " --> pdb=" O ASN w 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL w 122 " --> pdb=" O ALA w 118 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA w 123 " --> pdb=" O ALA w 119 " (cutoff:3.500A) Proline residue: w 138 - end of helix Processing helix chain 'x' and resid 25 through 34 Processing helix chain 'x' and resid 77 through 138 removed outlier: 3.709A pdb=" N THR x 82 " --> pdb=" O PRO x 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU x 93 " --> pdb=" O ASP x 89 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU x 98 " --> pdb=" O GLU x 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR x 101 " --> pdb=" O LYS x 97 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU x 102 " --> pdb=" O LEU x 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR x 106 " --> pdb=" O LEU x 102 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS x 107 " --> pdb=" O ASP x 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL x 112 " --> pdb=" O LYS x 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU x 121 " --> pdb=" O ASP x 117 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA x 124 " --> pdb=" O LYS x 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN x 125 " --> pdb=" O LEU x 121 " (cutoff:3.500A) Proline residue: x 138 - end of helix Processing helix chain 'y' and resid 16 through 30 Processing helix chain 'y' and resid 86 through 93 removed outlier: 4.091A pdb=" N ARG y 93 " --> pdb=" O GLU y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 114 through 117 No H-bonds generated for 'chain 'y' and resid 114 through 117' Processing helix chain 'y' and resid 121 through 130 Processing helix chain 'y' and resid 138 through 173 removed outlier: 3.690A pdb=" N ASN y 143 " --> pdb=" O GLN y 139 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR y 146 " --> pdb=" O ILE y 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE y 153 " --> pdb=" O GLN y 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL y 154 " --> pdb=" O THR y 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU y 155 " --> pdb=" O CYS y 151 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 300 through 302 Processing sheet with id= C, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= D, first strand: chain 'A' and resid 968 through 973 Processing sheet with id= E, first strand: chain 'A' and resid 1246 through 1251 removed outlier: 3.586A pdb=" N SER A1046 " --> pdb=" O PHE A1174 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= G, first strand: chain 'A' and resid 1257 through 1261 removed outlier: 6.699A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1624 through 1626 removed outlier: 3.579A pdb=" N VAL A1625 " --> pdb=" O LEU A1634 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1783 through 1788 removed outlier: 8.553A pdb=" N VAL A1773 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TRP A1733 " --> pdb=" O VAL A1773 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE A1775 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP A1735 " --> pdb=" O ILE A1775 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A1777 " --> pdb=" O ASP A1735 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN A1737 " --> pdb=" O ILE A1777 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= K, first strand: chain 'A' and resid 1985 through 1990 removed outlier: 6.669A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1859 through 1864 removed outlier: 4.752A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 133 through 138 removed outlier: 9.327A pdb=" N ILE B 134 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET B 209 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL B 136 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASN B 211 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B 138 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 213 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 234 through 240 removed outlier: 6.568A pdb=" N ALA B 262 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE B 237 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 264 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE B 239 " --> pdb=" O CYS B 264 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 266 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 536 through 538 removed outlier: 6.814A pdb=" N HIS B 471 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 488 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ILE B 561 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU B 545 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 542 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 474 through 477 removed outlier: 3.693A pdb=" N LYS B 474 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 668 through 670 Processing sheet with id= R, first strand: chain 'B' and resid 678 through 680 Processing sheet with id= S, first strand: chain 'B' and resid 774 through 776 removed outlier: 7.270A pdb=" N ILE B 775 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B 818 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER B 709 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 926 through 931 removed outlier: 7.040A pdb=" N GLN B 905 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE B 888 " --> pdb=" O GLN B 905 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 142 through 147 removed outlier: 6.909A pdb=" N GLY D 158 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL D 145 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 156 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE D 147 " --> pdb=" O TRP D 154 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TRP D 154 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 159 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP D 168 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU D 174 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 185 through 190 removed outlier: 6.944A pdb=" N VAL D 200 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL D 188 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE D 198 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL D 190 " --> pdb=" O TYR D 196 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR D 196 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 206 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP D 210 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE D 216 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 227 through 232 removed outlier: 6.790A pdb=" N ALA D 242 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL D 230 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 240 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 232 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU D 238 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 260 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP D 252 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 269 through 274 removed outlier: 7.015A pdb=" N SER D 284 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL D 272 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 282 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 281 " --> pdb=" O TRP D 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 302 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 313 through 316 removed outlier: 4.164A pdb=" N ALA D 313 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 363 through 367 removed outlier: 3.616A pdb=" N SER D 374 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 385 " --> pdb=" O PHE D 375 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP D 377 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS D 383 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 130 through 135 removed outlier: 6.872A pdb=" N ILE D 425 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL D 134 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 423 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 102 through 104 removed outlier: 3.765A pdb=" N ALA E 102 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU E 104 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 112 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 204 through 207 removed outlier: 3.644A pdb=" N ILE F 241 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG F 252 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 222 through 225 removed outlier: 4.439A pdb=" N CYS G 181 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 156 through 158 removed outlier: 3.986A pdb=" N ARG M 156 " --> pdb=" O VAL M 453 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 201 through 203 removed outlier: 4.281A pdb=" N THR M 186 " --> pdb=" O GLY M 182 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 243 through 245 removed outlier: 3.670A pdb=" N SER M 229 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU M 222 " --> pdb=" O ARG M 213 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG M 213 " --> pdb=" O LEU M 222 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'M' and resid 287 through 289 removed outlier: 3.770A pdb=" N PHE M 263 " --> pdb=" O TYR M 275 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 296 through 301 removed outlier: 6.847A pdb=" N SER M 311 " --> pdb=" O LEU M 297 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU M 299 " --> pdb=" O ILE M 309 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE M 309 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER M 312 " --> pdb=" O THR M 316 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR M 316 " --> pdb=" O SER M 312 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS M 329 " --> pdb=" O ILE M 319 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 360 through 364 removed outlier: 4.313A pdb=" N PHE M 341 " --> pdb=" O GLN M 354 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 389 through 391 removed outlier: 3.526A pdb=" N ASN M 419 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP M 411 " --> pdb=" O LEU M 417 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU M 417 " --> pdb=" O ASP M 411 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 279 through 282 removed outlier: 3.754A pdb=" N MET O 287 " --> pdb=" O ASP O 282 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 652 through 654 removed outlier: 8.558A pdb=" N ILE P 653 " --> pdb=" O PHE P 501 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL P 503 " --> pdb=" O ILE P 653 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL P 631 " --> pdb=" O LEU P 502 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE P 504 " --> pdb=" O VAL P 631 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL P 633 " --> pdb=" O ILE P 504 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY P 532 " --> pdb=" O VAL P 599 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 663 through 665 removed outlier: 3.688A pdb=" N ARG P 819 " --> pdb=" O LEU P 665 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP P 693 " --> pdb=" O TYR P 770 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL P 772 " --> pdb=" O ASP P 693 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU P 695 " --> pdb=" O VAL P 772 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP P 774 " --> pdb=" O LEU P 695 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE P 697 " --> pdb=" O ASP P 774 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 777 through 784 Processing sheet with id= AP, first strand: chain 'P' and resid 1041 through 1044 removed outlier: 4.330A pdb=" N TYR P1066 " --> pdb=" O ILE P1086 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 1071 through 1073 Processing sheet with id= AR, first strand: chain 'R' and resid 142 through 146 removed outlier: 3.872A pdb=" N LYS R 142 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS R 151 " --> pdb=" O ASP R 146 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'a' and resid 67 through 70 Processing sheet with id= AT, first strand: chain 'a' and resid 72 through 77 Processing sheet with id= AU, first strand: chain 'a' and resid 44 through 48 removed outlier: 3.907A pdb=" N VAL a 103 " --> pdb=" O SER a 47 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'b' and resid 71 through 73 removed outlier: 3.866A pdb=" N GLN b 52 " --> pdb=" O SER b 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER b 44 " --> pdb=" O GLN b 52 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN b 54 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU b 42 " --> pdb=" O ASN b 54 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'b' and resid 28 through 31 Processing sheet with id= AX, first strand: chain 'c' and resid 26 through 30 Processing sheet with id= AY, first strand: chain 'c' and resid 52 through 54 removed outlier: 4.090A pdb=" N VAL c 52 " --> pdb=" O LEU c 82 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU c 82 " --> pdb=" O VAL c 52 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'd' and resid 23 through 25 Processing sheet with id= BA, first strand: chain 'd' and resid 38 through 41 Processing sheet with id= BB, first strand: chain 'f' and resid 80 through 83 removed outlier: 6.184A pdb=" N CYS f 48 " --> pdb=" O LEU f 82 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG f 21 " --> pdb=" O VAL f 97 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL f 97 " --> pdb=" O ARG f 21 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU f 23 " --> pdb=" O THR f 95 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR f 95 " --> pdb=" O LEU f 23 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'f' and resid 43 through 45 Processing sheet with id= BD, first strand: chain 'g' and resid 69 through 73 removed outlier: 7.060A pdb=" N GLU g 22 " --> pdb=" O LYS g 70 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE g 72 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER g 20 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN g 43 " --> pdb=" O VAL g 34 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'g' and resid 48 through 50 Processing sheet with id= BF, first strand: chain 'h' and resid 24 through 26 Processing sheet with id= BG, first strand: chain 'h' and resid 84 through 87 removed outlier: 6.637A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'h' and resid 16 through 19 Processing sheet with id= BI, first strand: chain 'k' and resid 29 through 33 removed outlier: 3.807A pdb=" N LYS k 19 " --> pdb=" O ASP k 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP k 99 " --> pdb=" O LYS k 19 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG k 21 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL k 97 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'l' and resid 37 through 40 Processing sheet with id= BK, first strand: chain 'l' and resid 52 through 54 removed outlier: 3.973A pdb=" N VAL l 52 " --> pdb=" O LEU l 82 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU l 82 " --> pdb=" O VAL l 52 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'm' and resid 57 through 59 removed outlier: 4.073A pdb=" N LYS m 30 " --> pdb=" O TYR m 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR m 80 " --> pdb=" O LYS m 30 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'm' and resid 51 through 53 Processing sheet with id= BN, first strand: chain 'n' and resid 26 through 28 removed outlier: 3.529A pdb=" N SER n 70 " --> pdb=" O ASN n 18 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'o' and resid 18 through 20 removed outlier: 3.501A pdb=" N GLY o 31 " --> pdb=" O VAL o 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR o 28 " --> pdb=" O THR o 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG o 30 " --> pdb=" O ILE o 48 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'o' and resid 42 through 45 removed outlier: 3.507A pdb=" N VAL o 42 " --> pdb=" O VAL o 64 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'o' and resid 21 through 23 Processing sheet with id= BR, first strand: chain 'q' and resid 43 through 47 removed outlier: 3.824A pdb=" N GLU q 74 " --> pdb=" O ARG q 89 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG q 89 " --> pdb=" O GLU q 74 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP q 76 " --> pdb=" O ARG q 87 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG q 87 " --> pdb=" O TRP q 76 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'q' and resid 57 through 60 removed outlier: 6.851A pdb=" N VAL q 68 " --> pdb=" O LYS q 59 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'r' and resid 30 through 32 removed outlier: 3.847A pdb=" N ALA r 72 " --> pdb=" O VAL r 32 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'r' and resid 92 through 94 removed outlier: 3.922A pdb=" N GLU r 92 " --> pdb=" O LEU r 99 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS r 97 " --> pdb=" O PHE r 94 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'u' and resid 13 through 15 Processing sheet with id= BW, first strand: chain 'u' and resid 197 through 200 Processing sheet with id= BX, first strand: chain 'u' and resid 210 through 216 Processing sheet with id= BY, first strand: chain 'u' and resid 248 through 251 removed outlier: 3.514A pdb=" N ILE u 248 " --> pdb=" O LEU u 260 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP u 270 " --> pdb=" O VAL u 276 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL u 276 " --> pdb=" O ASP u 270 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'u' and resid 288 through 292 removed outlier: 6.515A pdb=" N ALA u 305 " --> pdb=" O ILE u 289 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET u 291 " --> pdb=" O ILE u 303 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE u 303 " --> pdb=" O MET u 291 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE u 313 " --> pdb=" O ILE u 323 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE u 323 " --> pdb=" O PHE u 313 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER u 315 " --> pdb=" O GLN u 321 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN u 321 " --> pdb=" O SER u 315 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'u' and resid 335 through 338 Processing sheet with id= CB, first strand: chain 'u' and resid 397 through 401 Processing sheet with id= CC, first strand: chain 'u' and resid 424 through 428 removed outlier: 6.236A pdb=" N LYS u 449 " --> pdb=" O LYS u 459 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS u 459 " --> pdb=" O LYS u 449 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'u' and resid 476 through 482 removed outlier: 3.801A pdb=" N GLY u 482 " --> pdb=" O GLY u 485 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE u 486 " --> pdb=" O LEU u 501 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA u 500 " --> pdb=" O LEU u 182 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU u 182 " --> pdb=" O ALA u 500 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR u 502 " --> pdb=" O LEU u 180 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU u 180 " --> pdb=" O THR u 502 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'v' and resid 13 through 15 Processing sheet with id= CF, first strand: chain 'w' and resid 13 through 15 Processing sheet with id= CG, first strand: chain 'w' and resid 197 through 200 Processing sheet with id= CH, first strand: chain 'w' and resid 210 through 216 Processing sheet with id= CI, first strand: chain 'w' and resid 248 through 251 removed outlier: 3.512A pdb=" N ILE w 248 " --> pdb=" O LEU w 260 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP w 270 " --> pdb=" O VAL w 276 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL w 276 " --> pdb=" O ASP w 270 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'w' and resid 288 through 292 removed outlier: 6.514A pdb=" N ALA w 305 " --> pdb=" O ILE w 289 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET w 291 " --> pdb=" O ILE w 303 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE w 303 " --> pdb=" O MET w 291 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE w 313 " --> pdb=" O ILE w 323 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE w 323 " --> pdb=" O PHE w 313 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER w 315 " --> pdb=" O GLN w 321 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN w 321 " --> pdb=" O SER w 315 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'w' and resid 335 through 338 Processing sheet with id= CL, first strand: chain 'w' and resid 397 through 401 Processing sheet with id= CM, first strand: chain 'w' and resid 424 through 428 removed outlier: 6.235A pdb=" N LYS w 449 " --> pdb=" O LYS w 459 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS w 459 " --> pdb=" O LYS w 449 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'w' and resid 476 through 482 removed outlier: 3.800A pdb=" N GLY w 482 " --> pdb=" O GLY w 485 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE w 486 " --> pdb=" O LEU w 501 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA w 500 " --> pdb=" O LEU w 182 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU w 182 " --> pdb=" O ALA w 500 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR w 502 " --> pdb=" O LEU w 180 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU w 180 " --> pdb=" O THR w 502 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'x' and resid 13 through 16 removed outlier: 4.063A pdb=" N THR x 21 " --> pdb=" O SER x 16 " (cutoff:3.500A) 3266 hydrogen bonds defined for protein. 9198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 272 hydrogen bonds 500 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 221 stacking parallelities Total time for adding SS restraints: 52.49 Time building geometry restraints manager: 29.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 13077 1.30 - 1.43: 23352 1.43 - 1.56: 47155 1.56 - 1.69: 940 1.69 - 1.82: 400 Bond restraints: 84924 Sorted by residual: bond pdb=" C LEU v 109 " pdb=" N SER v 110 " ideal model delta sigma weight residual 1.335 1.442 -0.107 1.31e-02 5.83e+03 6.63e+01 bond pdb=" C1' U e 9 " pdb=" N1 U e 9 " ideal model delta sigma weight residual 1.480 1.589 -0.109 1.50e-02 4.44e+03 5.24e+01 bond pdb=" C1' U e -13 " pdb=" N1 U e -13 " ideal model delta sigma weight residual 1.480 1.585 -0.105 1.50e-02 4.44e+03 4.91e+01 bond pdb=" C1' U e -11 " pdb=" N1 U e -11 " ideal model delta sigma weight residual 1.480 1.574 -0.094 1.50e-02 4.44e+03 3.90e+01 bond pdb=" C SER v 134 " pdb=" O SER v 134 " ideal model delta sigma weight residual 1.237 1.168 0.069 1.19e-02 7.06e+03 3.35e+01 ... (remaining 84919 not shown) Histogram of bond angle deviations from ideal: 92.77 - 101.51: 417 101.51 - 110.25: 22717 110.25 - 118.98: 49003 118.98 - 127.72: 43792 127.72 - 136.46: 1382 Bond angle restraints: 117311 Sorted by residual: angle pdb=" CA SER w 134 " pdb=" C SER w 134 " pdb=" O SER w 134 " ideal model delta sigma weight residual 120.70 103.49 17.21 1.03e+00 9.43e-01 2.79e+02 angle pdb=" CA SER v 134 " pdb=" C SER v 134 " pdb=" O SER v 134 " ideal model delta sigma weight residual 120.42 108.16 12.26 1.06e+00 8.90e-01 1.34e+02 angle pdb=" C LEU v 137 " pdb=" N PRO v 138 " pdb=" CA PRO v 138 " ideal model delta sigma weight residual 119.05 130.36 -11.31 1.11e+00 8.12e-01 1.04e+02 angle pdb=" C LEU y 132 " pdb=" N PRO y 133 " pdb=" CA PRO y 133 " ideal model delta sigma weight residual 119.84 132.53 -12.69 1.25e+00 6.40e-01 1.03e+02 angle pdb=" O SER w 134 " pdb=" C SER w 134 " pdb=" N LYS w 135 " ideal model delta sigma weight residual 122.09 132.30 -10.21 1.08e+00 8.57e-01 8.94e+01 ... (remaining 117306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 49901 35.98 - 71.97: 1132 71.97 - 107.95: 131 107.95 - 143.93: 15 143.93 - 179.92: 13 Dihedral angle restraints: 51192 sinusoidal: 21327 harmonic: 29865 Sorted by residual: dihedral pdb=" CA ASP B 777 " pdb=" C ASP B 777 " pdb=" N THR B 778 " pdb=" CA THR B 778 " ideal model delta harmonic sigma weight residual 180.00 127.46 52.54 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ILE A 774 " pdb=" C ILE A 774 " pdb=" N ARG A 775 " pdb=" CA ARG A 775 " ideal model delta harmonic sigma weight residual -180.00 -127.99 -52.01 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA HIS A 542 " pdb=" C HIS A 542 " pdb=" N ASN A 543 " pdb=" CA ASN A 543 " ideal model delta harmonic sigma weight residual -180.00 -128.85 -51.15 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 51189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.929: 14083 0.929 - 1.858: 0 1.858 - 2.787: 0 2.787 - 3.716: 0 3.716 - 4.644: 4 Chirality restraints: 14087 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.13 -4.64 2.00e-01 2.50e+01 5.39e+02 chirality pdb=" C5 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O15 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.42 2.08 -4.50 2.00e-01 2.50e+01 5.05e+02 chirality pdb=" C1 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O11 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.32 -2.12 4.44 2.00e-01 2.50e+01 4.92e+02 ... (remaining 14084 not shown) Planarity restraints: 13596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER u 134 " -0.038 2.00e-02 2.50e+03 7.54e-02 5.68e+01 pdb=" C SER u 134 " 0.130 2.00e-02 2.50e+03 pdb=" O SER u 134 " -0.047 2.00e-02 2.50e+03 pdb=" N LYS u 135 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU v 109 " -0.038 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" C LEU v 109 " 0.128 2.00e-02 2.50e+03 pdb=" O LEU v 109 " -0.052 2.00e-02 2.50e+03 pdb=" N SER v 110 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS w 3 " 0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C CYS w 3 " -0.103 2.00e-02 2.50e+03 pdb=" O CYS w 3 " 0.039 2.00e-02 2.50e+03 pdb=" N ALA w 4 " 0.035 2.00e-02 2.50e+03 ... (remaining 13593 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 15 1.80 - 2.57: 546 2.57 - 3.35: 98851 3.35 - 4.12: 197268 4.12 - 4.90: 349444 Nonbonded interactions: 646124 Sorted by model distance: nonbonded pdb=" P G i 1 " pdb=" O2' A i 515 " model vdw 1.020 3.400 nonbonded pdb=" O3' G 2 100 " pdb=" CZ ARG k 11 " model vdw 1.052 3.270 nonbonded pdb=" CB ILE v 77 " pdb=" CB LYS y 122 " model vdw 1.254 3.870 nonbonded pdb=" O3' G 2 100 " pdb=" NH1 ARG k 11 " model vdw 1.255 2.520 nonbonded pdb=" OP1 U 2 102 " pdb=" CE LYS p 8 " model vdw 1.263 3.440 ... (remaining 646119 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' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 108)) selection = chain 'q' } ncs_group { reference = chain 'b' selection = chain 'm' } ncs_group { reference = chain 'c' selection = chain 'l' } ncs_group { reference = (chain 'd' and (resid 2 through 40 or (resid 41 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'f' and (resid 4 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 100)) selection = chain 'k' } ncs_group { reference = (chain 'g' and (resid 4 through 51 or resid 56 through 85)) selection = chain 'o' } ncs_group { reference = (chain 'h' and (resid 1 through 98 or (resid 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 106)) selection = chain 'p' } ncs_group { reference = (chain 'u' and (resid 1 through 51 or resid 78 through 503)) selection = (chain 'w' and (resid 1 through 139 or resid 171 through 503)) } ncs_group { reference = (chain 'v' and resid 1 through 139) selection = (chain 'x' and (resid 1 through 51 or resid 76 through 139)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.290 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: 0.080 Extract box with map and model: 16.580 Check model and map are aligned: 0.930 Set scattering table: 0.560 Process input model: 216.530 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.009 0.112 84924 Z= 0.610 Angle : 1.232 20.156 117311 Z= 0.728 Chirality : 0.102 4.644 14087 Planarity : 0.008 0.088 13596 Dihedral : 15.227 179.918 31652 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.28 % Favored : 93.22 % Rotamer: Outliers : 1.27 % Allowed : 5.67 % Favored : 93.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.74 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.07), residues: 9709 helix: -2.30 (0.06), residues: 4097 sheet: -1.57 (0.13), residues: 1352 loop : -2.71 (0.08), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP T 205 HIS 0.020 0.003 HIS A 828 PHE 0.058 0.004 PHE T 172 TYR 0.082 0.004 TYR T 139 ARG 0.024 0.002 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1042 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 16 residues processed: 1116 average time/residue: 0.8016 time to fit residues: 1517.2541 Evaluate side-chains 641 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 625 time to evaluate : 6.376 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.7241 time to fit residues: 28.9971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 879 optimal weight: 4.9990 chunk 789 optimal weight: 9.9990 chunk 437 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 chunk 532 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 815 optimal weight: 8.9990 chunk 315 optimal weight: 0.0770 chunk 496 optimal weight: 6.9990 chunk 607 optimal weight: 3.9990 chunk 945 optimal weight: 6.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 310 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 658 ASN A 676 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN A 961 GLN A1030 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1455 GLN A1471 GLN A1529 ASN A1548 GLN A1687 HIS A1782 ASN A1809 ASN ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1831 GLN A1876 ASN A1895 HIS A2086 GLN B 101 GLN B 103 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 294 ASN B 358 ASN B 511 GLN B 514 GLN B 647 ASN B 764 ASN B 869 HIS B 960 ASN B1004 ASN D 126 HIS D 160 ASN D 445 ASN E 48 GLN E 103 ASN E 110 HIS G 39 GLN G 44 ASN ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS L 14 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN L 104 GLN L 354 HIS L 390 HIS L 441 ASN L 457 HIS M 219 GLN M 261 HIS M 325 ASN M 380 HIS ** N 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 203 HIS N 208 HIS N 246 ASN N 247 HIS ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 HIS P 960 HIS P 989 HIS P1082 GLN R 200 ASN R 204 ASN T 61 ASN T 183 ASN T 212 HIS b 24 ASN h 94 GLN l 86 ASN m 24 ASN n 18 ASN n 53 ASN p 14 GLN p 21 ASN p 86 ASN p 94 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 84924 Z= 0.212 Angle : 0.656 14.789 117311 Z= 0.339 Chirality : 0.045 0.848 14087 Planarity : 0.005 0.066 13596 Dihedral : 15.607 177.705 16753 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.57 % Favored : 95.21 % Rotamer: Outliers : 2.48 % Allowed : 9.48 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.82 (0.08), residues: 9709 helix: -0.24 (0.08), residues: 4103 sheet: -1.04 (0.13), residues: 1412 loop : -2.23 (0.09), residues: 4194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP p 26 HIS 0.014 0.001 HIS B 143 PHE 0.024 0.002 PHE U 748 TYR 0.026 0.001 TYR m 80 ARG 0.007 0.001 ARG k 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 678 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 63 residues processed: 800 average time/residue: 0.7606 time to fit residues: 1069.2400 Evaluate side-chains 647 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 584 time to evaluate : 6.597 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 1 residues processed: 63 average time/residue: 0.6170 time to fit residues: 82.6127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 525 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 786 optimal weight: 10.0000 chunk 643 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 947 optimal weight: 50.0000 chunk 1023 optimal weight: 50.0000 chunk 843 optimal weight: 6.9990 chunk 939 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 759 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 343 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 659 HIS A 961 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS A1376 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN A1592 HIS A1907 GLN A2018 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN F 141 ASN ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN L 69 ASN L 104 GLN L 441 ASN ** N 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 HIS O 309 HIS O 327 HIS P 933 GLN S 41 GLN ** T 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 52 HIS c 15 ASN l 86 ASN o 61 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 84924 Z= 0.429 Angle : 0.742 16.299 117311 Z= 0.379 Chirality : 0.048 0.586 14087 Planarity : 0.005 0.070 13596 Dihedral : 15.513 178.854 16753 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.93 % Favored : 93.83 % Rotamer: Outliers : 3.09 % Allowed : 11.59 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.23 (0.08), residues: 9709 helix: 0.42 (0.08), residues: 4082 sheet: -0.94 (0.13), residues: 1432 loop : -2.04 (0.09), residues: 4195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP U 781 HIS 0.011 0.002 HIS B 471 PHE 0.035 0.003 PHE U 646 TYR 0.030 0.002 TYR A 689 ARG 0.011 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 605 time to evaluate : 6.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 94 residues processed: 771 average time/residue: 0.7546 time to fit residues: 1020.2843 Evaluate side-chains 654 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 560 time to evaluate : 6.548 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 1 residues processed: 94 average time/residue: 0.6530 time to fit residues: 122.8897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 935 optimal weight: 6.9990 chunk 712 optimal weight: 30.0000 chunk 491 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 451 optimal weight: 30.0000 chunk 635 optimal weight: 4.9990 chunk 950 optimal weight: 30.0000 chunk 1006 optimal weight: 30.0000 chunk 496 optimal weight: 6.9990 chunk 900 optimal weight: 40.0000 chunk 271 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN A 961 GLN A 997 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1471 GLN A1559 HIS ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1907 GLN ** A2038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN F 81 HIS F 106 ASN G 252 HIS ** H 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** N 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 HIS P1126 ASN ** T 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 84924 Z= 0.395 Angle : 0.685 15.301 117311 Z= 0.352 Chirality : 0.046 0.496 14087 Planarity : 0.005 0.067 13596 Dihedral : 15.402 179.287 16753 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.28 % Rotamer: Outliers : 2.94 % Allowed : 12.66 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.08), residues: 9709 helix: 0.81 (0.08), residues: 4075 sheet: -0.79 (0.13), residues: 1439 loop : -1.92 (0.09), residues: 4195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 221 HIS 0.009 0.001 HIS D 194 PHE 0.028 0.002 PHE U 646 TYR 0.026 0.002 TYR A 689 ARG 0.009 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 581 time to evaluate : 6.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 192 outliers final: 97 residues processed: 736 average time/residue: 0.7590 time to fit residues: 984.4543 Evaluate side-chains 647 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 550 time to evaluate : 6.543 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 1 residues processed: 97 average time/residue: 0.6245 time to fit residues: 123.8161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 838 optimal weight: 6.9990 chunk 571 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 749 optimal weight: 3.9990 chunk 415 optimal weight: 0.7980 chunk 858 optimal weight: 5.9990 chunk 695 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 513 optimal weight: 2.9990 chunk 903 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1652 HIS ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 HIS P1126 ASN ** T 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 84924 Z= 0.326 Angle : 0.649 14.667 117311 Z= 0.331 Chirality : 0.045 0.432 14087 Planarity : 0.005 0.064 13596 Dihedral : 15.289 177.817 16753 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 2.29 % Allowed : 14.27 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.09), residues: 9709 helix: 1.10 (0.08), residues: 4070 sheet: -0.66 (0.13), residues: 1411 loop : -1.81 (0.09), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 709 HIS 0.006 0.001 HIS B 471 PHE 0.027 0.002 PHE U 646 TYR 0.021 0.002 TYR A 689 ARG 0.007 0.001 ARG A1268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 581 time to evaluate : 6.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 52 residues processed: 710 average time/residue: 0.7584 time to fit residues: 959.4309 Evaluate side-chains 600 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 548 time to evaluate : 6.484 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 1 residues processed: 52 average time/residue: 0.6161 time to fit residues: 70.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1041 random chunks: chunk 338 optimal weight: 1.9990 chunk 906 optimal weight: 30.0000 chunk 198 optimal weight: 5.9990 chunk 590 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 1007 optimal weight: 9.9990 chunk 836 optimal weight: 30.0000 chunk 466 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 333 optimal weight: 0.7980 chunk 528 optimal weight: 0.0170 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN F 141 ASN ** G 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS L 104 GLN ** O 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 HIS P1126 ASN ** T 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 84924 Z= 0.187 Angle : 0.573 15.892 117311 Z= 0.293 Chirality : 0.041 0.370 14087 Planarity : 0.004 0.053 13596 Dihedral : 15.115 179.481 16753 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 1.54 % Allowed : 15.05 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.20 (0.09), residues: 9709 helix: 1.46 (0.08), residues: 4071 sheet: -0.47 (0.13), residues: 1413 loop : -1.66 (0.09), residues: 4225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 823 HIS 0.007 0.001 HIS A 181 PHE 0.028 0.001 PHE U 646 TYR 0.036 0.001 TYR m 80 ARG 0.007 0.000 ARG U 689 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19418 Ramachandran restraints generated. 9709 Oldfield, 0 Emsley, 9709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 603 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 48 residues processed: 676 average time/residue: 0.8089 time to fit residues: 957.6134 Evaluate side-chains 605 residues out of total 9028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 557 time to evaluate : 6.512 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.6243 time to fit residues: 66.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.2487 > 50: distance: 62 - 66: 5.208 distance: 66 - 67: 11.054 distance: 67 - 68: 17.323 distance: 67 - 70: 24.605 distance: 68 - 69: 30.849 distance: 68 - 71: 22.036 distance: 71 - 72: 13.216 distance: 72 - 73: 24.863 distance: 72 - 75: 12.539 distance: 73 - 74: 7.976 distance: 73 - 80: 14.878 distance: 75 - 76: 22.523 distance: 76 - 77: 7.535 distance: 77 - 78: 13.266 distance: 78 - 79: 12.159 distance: 80 - 81: 9.529 distance: 81 - 82: 12.641 distance: 81 - 84: 8.912 distance: 82 - 83: 8.726 distance: 82 - 88: 18.576 distance: 84 - 85: 15.102 distance: 85 - 86: 9.297 distance: 85 - 87: 17.572 distance: 88 - 89: 7.278 distance: 89 - 90: 11.844 distance: 89 - 92: 17.811 distance: 90 - 91: 11.222 distance: 90 - 97: 14.867 distance: 92 - 93: 21.071 distance: 93 - 94: 14.838 distance: 94 - 95: 5.333 distance: 94 - 96: 16.117 distance: 97 - 98: 11.982 distance: 98 - 99: 11.306 distance: 98 - 101: 26.074 distance: 99 - 100: 26.262 distance: 99 - 105: 17.304 distance: 101 - 102: 23.459 distance: 102 - 103: 20.750 distance: 102 - 104: 4.903 distance: 105 - 106: 9.931 distance: 106 - 107: 7.626 distance: 106 - 109: 26.760 distance: 107 - 108: 22.427 distance: 107 - 111: 17.206 distance: 109 - 110: 18.447 distance: 111 - 112: 18.281 distance: 112 - 113: 16.398 distance: 112 - 115: 7.497 distance: 113 - 125: 11.613 distance: 115 - 116: 19.779 distance: 116 - 117: 10.005 distance: 116 - 118: 15.125 distance: 117 - 119: 4.715 distance: 118 - 120: 21.492 distance: 118 - 121: 17.013 distance: 119 - 120: 10.708 distance: 120 - 122: 7.776 distance: 121 - 123: 3.684 distance: 122 - 124: 13.432 distance: 123 - 124: 14.391 distance: 125 - 126: 25.075 distance: 126 - 127: 19.803 distance: 126 - 129: 26.531 distance: 127 - 128: 7.403 distance: 127 - 136: 42.988 distance: 129 - 130: 15.614 distance: 130 - 131: 11.786 distance: 131 - 132: 15.080 distance: 132 - 133: 11.019 distance: 133 - 134: 30.135 distance: 133 - 135: 12.174 distance: 136 - 137: 20.849 distance: 137 - 138: 19.680 distance: 137 - 140: 15.522 distance: 138 - 139: 21.504 distance: 138 - 144: 23.872 distance: 139 - 164: 8.430 distance: 140 - 141: 14.242 distance: 141 - 142: 9.088 distance: 141 - 143: 10.372 distance: 144 - 145: 17.847 distance: 145 - 146: 14.862 distance: 145 - 148: 14.480 distance: 146 - 147: 8.278 distance: 146 - 150: 11.772 distance: 147 - 174: 3.887 distance: 148 - 149: 19.024