Starting phenix.real_space_refine on Sun Apr 7 00:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9z_37386/04_2024/8w9z_37386.pdb" } resolution = 3.0 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 50 atoms to isotropic. 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 Fe 2 7.16 5 Zn 1 6.06 5 Mg 1 5.21 5 S 258 5.16 5 C 38325 2.51 5 N 10707 2.21 5 O 11231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "a ARG 64": "NH1" <-> "NH2" Residue "a ARG 155": "NH1" <-> "NH2" Residue "a ARG 180": "NH1" <-> "NH2" Residue "a GLU 197": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1047": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C GLU 629": "OE1" <-> "OE2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c ARG 120": "NH1" <-> "NH2" Residue "c ARG 186": "NH1" <-> "NH2" Residue "c ARG 279": "NH1" <-> "NH2" Residue "c ARG 1303": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 612": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "E ARG 681": "NH1" <-> "NH2" Residue "E ARG 684": "NH1" <-> "NH2" Residue "E ARG 749": "NH1" <-> "NH2" Residue "E GLU 753": "OE1" <-> "OE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 520": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 531": "NH1" <-> "NH2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "H ARG 211": "NH1" <-> "NH2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 328": "NH1" <-> "NH2" Residue "H ARG 408": "NH1" <-> "NH2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I ARG 273": "NH1" <-> "NH2" Residue "I ARG 302": "NH1" <-> "NH2" Residue "I ARG 358": "NH1" <-> "NH2" Residue "I ARG 359": "NH1" <-> "NH2" Residue "I ARG 445": "NH1" <-> "NH2" Residue "i ARG 299": "NH1" <-> "NH2" Residue "i ARG 438": "NH1" <-> "NH2" Residue "i ARG 612": "NH1" <-> "NH2" Residue "i ARG 613": "NH1" <-> "NH2" Residue "i ARG 642": "NH1" <-> "NH2" Residue "J PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 242": "OE1" <-> "OE2" Residue "J TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 245": "OE1" <-> "OE2" Residue "L GLU 282": "OE1" <-> "OE2" Residue "M PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 171": "NH1" <-> "NH2" Residue "N ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 60525 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2202 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "a" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2441 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6820 Classifications: {'peptide': 909} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 39, 'TRANS': 869} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 450 Unresolved non-hydrogen angles: 569 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 263 Chain: "C" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4431 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 31, 'TRANS': 560} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 238 Chain: "c" Number of atoms: 8086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 8086 Classifications: {'peptide': 1174} Incomplete info: {'truncation_to_alanine': 364} Link IDs: {'PTRANS': 54, 'TRANS': 1119} Chain breaks: 6 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1284 Unresolved non-hydrogen angles: 1625 Unresolved non-hydrogen dihedrals: 1059 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 8, 'TYR:plan': 13, 'ASN:plan1': 30, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 14, 'GLU:plan': 21, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 682 Chain: "D" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5088 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 621} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 4534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 4534 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'PTRANS': 18, 'TRANS': 681} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1082 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 14, 'GLU:plan': 32, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 611 Chain: "F" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4233 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 33, 'TRANS': 510} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 220 Chain: "G" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1727 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2110 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "I" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2897 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 353} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "i" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2983 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 362} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3368 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 396} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "K" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1779 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1475 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 15, 'TRANS': 218} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 20, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 269 Chain: "M" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 2982 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 354} Link IDs: {'PTRANS': 23, 'TRANS': 513} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1219 Unresolved non-hydrogen angles: 1560 Unresolved non-hydrogen dihedrals: 974 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 12, 'ASP:plan': 34, 'PHE:plan': 14, 'GLU:plan': 38, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 649 Chain: "O" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 887 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.64, per 1000 atoms: 0.39 Number of scatterers: 60525 At special positions: 0 Unit cell: (232.1, 253, 170.5, 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 1 29.99 Fe 2 26.01 S 258 16.00 Mg 1 11.99 O 11231 8.00 N 10707 7.00 C 38325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS m 101 " - pdb=" SG CYS m 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.54 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 536 " 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15410 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 70 sheets defined 45.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 removed outlier: 4.170A pdb=" N THR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.610A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.563A pdb=" N LEU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'a' and resid 40 through 54 removed outlier: 3.855A pdb=" N THR a 44 " --> pdb=" O GLY a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 93 removed outlier: 3.583A pdb=" N GLU a 93 " --> pdb=" O MET a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 227 Processing helix chain 'a' and resid 228 through 231 Processing helix chain 'a' and resid 253 through 264 removed outlier: 3.778A pdb=" N ILE a 261 " --> pdb=" O LEU a 257 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS a 262 " --> pdb=" O ALA a 258 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS a 264 " --> pdb=" O LEU a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 272 removed outlier: 3.594A pdb=" N SER a 271 " --> pdb=" O ILE a 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE a 272 " --> pdb=" O ALA a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 272' Processing helix chain 'a' and resid 280 through 290 Processing helix chain 'a' and resid 294 through 301 removed outlier: 3.607A pdb=" N ASN a 301 " --> pdb=" O ASP a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 309 removed outlier: 4.061A pdb=" N LYS a 308 " --> pdb=" O GLU a 304 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE a 309 " --> pdb=" O ASP a 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 304 through 309' Processing helix chain 'a' and resid 314 through 328 removed outlier: 3.662A pdb=" N LYS a 318 " --> pdb=" O SER a 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 removed outlier: 5.621A pdb=" N LEU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.601A pdb=" N VAL B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.805A pdb=" N PHE B 204 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.584A pdb=" N ARG B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.646A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 316 through 347 removed outlier: 3.506A pdb=" N LEU B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 358 through 372 removed outlier: 4.009A pdb=" N THR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 removed outlier: 3.591A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 387 " --> pdb=" O PRO B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.275A pdb=" N ARG B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 412' Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.693A pdb=" N TYR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.530A pdb=" N TYR B 476 " --> pdb=" O ARG B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.636A pdb=" N GLN B 522 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 523' Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 551 removed outlier: 3.937A pdb=" N ARG B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 576 removed outlier: 4.383A pdb=" N GLY B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 removed outlier: 3.697A pdb=" N TYR B 679 " --> pdb=" O GLU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.654A pdb=" N SER B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 879 removed outlier: 3.735A pdb=" N PHE B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.813A pdb=" N ARG B 890 " --> pdb=" O PHE B 887 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 891 " --> pdb=" O ASP B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 891' Processing helix chain 'B' and resid 894 through 911 removed outlier: 3.570A pdb=" N LYS B 898 " --> pdb=" O GLU B 894 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 998 through 1011 Processing helix chain 'B' and resid 1036 through 1048 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.181A pdb=" N ALA C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.960A pdb=" N LEU C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 150 removed outlier: 4.071A pdb=" N LEU C 144 " --> pdb=" O PRO C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 4.055A pdb=" N PHE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 199 removed outlier: 4.298A pdb=" N ASN C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.673A pdb=" N ILE C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 229 removed outlier: 3.908A pdb=" N GLU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 262 removed outlier: 3.566A pdb=" N ASP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 270 removed outlier: 3.567A pdb=" N TRP C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 270' Processing helix chain 'C' and resid 297 through 320 removed outlier: 3.675A pdb=" N SER C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.745A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.509A pdb=" N GLN C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 441 through 452 removed outlier: 3.585A pdb=" N TRP C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 Processing helix chain 'C' and resid 509 through 519 Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.561A pdb=" N MET C 524 " --> pdb=" O PHE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 552 removed outlier: 4.520A pdb=" N GLY C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.608A pdb=" N ASN C 566 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 601 Processing helix chain 'C' and resid 663 through 685 removed outlier: 3.867A pdb=" N ILE C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 30 removed outlier: 3.559A pdb=" N ASP c 28 " --> pdb=" O SER c 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 54 removed outlier: 3.684A pdb=" N HIS c 37 " --> pdb=" O ALA c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 68 through 88 removed outlier: 3.585A pdb=" N HIS c 87 " --> pdb=" O GLU c 83 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR c 88 " --> pdb=" O LYS c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 122 removed outlier: 3.912A pdb=" N THR c 107 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN c 116 " --> pdb=" O ARG c 112 " (cutoff:3.500A) Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 134 Processing helix chain 'c' and resid 139 through 148 Processing helix chain 'c' and resid 174 through 210 removed outlier: 3.684A pdb=" N TYR c 183 " --> pdb=" O ILE c 179 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY c 184 " --> pdb=" O ILE c 180 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA c 193 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR c 201 " --> pdb=" O SER c 197 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL c 210 " --> pdb=" O LEU c 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 245 removed outlier: 3.737A pdb=" N PHE c 240 " --> pdb=" O PRO c 236 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU c 244 " --> pdb=" O PHE c 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 268 through 279 Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.638A pdb=" N CYS c 291 " --> pdb=" O PRO c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 298 through 303 Processing helix chain 'c' and resid 317 through 328 Processing helix chain 'c' and resid 329 through 331 No H-bonds generated for 'chain 'c' and resid 329 through 331' Processing helix chain 'c' and resid 487 through 491 Processing helix chain 'c' and resid 563 through 568 Processing helix chain 'c' and resid 616 through 620 Processing helix chain 'c' and resid 881 through 885 Processing helix chain 'c' and resid 898 through 902 Processing helix chain 'c' and resid 906 through 916 removed outlier: 3.820A pdb=" N SER c 910 " --> pdb=" O SER c 906 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS c 913 " --> pdb=" O TYR c 909 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA c 914 " --> pdb=" O SER c 910 " (cutoff:3.500A) Processing helix chain 'c' and resid 931 through 935 removed outlier: 4.226A pdb=" N LYS c 935 " --> pdb=" O ASN c 932 " (cutoff:3.500A) Processing helix chain 'c' and resid 1004 through 1009 removed outlier: 3.809A pdb=" N TYR c1008 " --> pdb=" O LEU c1004 " (cutoff:3.500A) Processing helix chain 'c' and resid 1011 through 1016 removed outlier: 3.546A pdb=" N LYS c1015 " --> pdb=" O LEU c1011 " (cutoff:3.500A) Processing helix chain 'c' and resid 1085 through 1089 removed outlier: 4.071A pdb=" N SER c1088 " --> pdb=" O PRO c1085 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY c1089 " --> pdb=" O LEU c1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1085 through 1089' Processing helix chain 'c' and resid 1147 through 1154 Processing helix chain 'c' and resid 1157 through 1162 removed outlier: 3.986A pdb=" N ILE c1161 " --> pdb=" O SER c1157 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER c1162 " --> pdb=" O VAL c1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1157 through 1162' Processing helix chain 'c' and resid 1162 through 1179 removed outlier: 3.544A pdb=" N GLU c1166 " --> pdb=" O SER c1162 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS c1174 " --> pdb=" O GLU c1170 " (cutoff:3.500A) Processing helix chain 'c' and resid 1182 through 1211 removed outlier: 3.755A pdb=" N PHE c1186 " --> pdb=" O ILE c1182 " (cutoff:3.500A) Processing helix chain 'c' and resid 1217 through 1229 removed outlier: 3.998A pdb=" N LEU c1221 " --> pdb=" O HIS c1217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE c1224 " --> pdb=" O HIS c1220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN c1227 " --> pdb=" O ILE c1223 " (cutoff:3.500A) Processing helix chain 'c' and resid 1251 through 1261 Processing helix chain 'c' and resid 1294 through 1304 removed outlier: 3.608A pdb=" N ALA c1300 " --> pdb=" O VAL c1296 " (cutoff:3.500A) Processing helix chain 'c' and resid 1312 through 1319 Processing helix chain 'D' and resid 65 through 83 removed outlier: 3.806A pdb=" N VAL D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.839A pdb=" N VAL D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.753A pdb=" N GLY D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 removed outlier: 3.822A pdb=" N GLU D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.564A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.613A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU D 161 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 189 through 202 removed outlier: 3.623A pdb=" N ALA D 193 " --> pdb=" O HIS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.519A pdb=" N ILE D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 Processing helix chain 'D' and resid 243 through 255 Processing helix chain 'D' and resid 259 through 272 removed outlier: 4.273A pdb=" N ALA D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.629A pdb=" N ALA D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 336 through 350 removed outlier: 3.560A pdb=" N ALA D 340 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 365 through 377 Processing helix chain 'D' and resid 379 through 389 Processing helix chain 'D' and resid 430 through 439 Processing helix chain 'D' and resid 458 through 462 removed outlier: 3.837A pdb=" N GLU D 462 " --> pdb=" O PRO D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 496 removed outlier: 3.674A pdb=" N ASN D 495 " --> pdb=" O LYS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 520 removed outlier: 4.607A pdb=" N ILE D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 514 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 599 Processing helix chain 'D' and resid 606 through 615 removed outlier: 3.755A pdb=" N TRP D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 745 removed outlier: 3.548A pdb=" N ALA D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 753 Processing helix chain 'D' and resid 755 through 761 Processing helix chain 'D' and resid 765 through 770 removed outlier: 4.027A pdb=" N ASN D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 796 removed outlier: 3.702A pdb=" N LYS D 787 " --> pdb=" O GLU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 814 removed outlier: 3.652A pdb=" N CYS D 804 " --> pdb=" O THR D 800 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 807 " --> pdb=" O ASP D 803 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 831 removed outlier: 3.695A pdb=" N LEU D 824 " --> pdb=" O PHE D 820 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 849 removed outlier: 3.826A pdb=" N TYR D 839 " --> pdb=" O GLY D 835 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 840 " --> pdb=" O SER D 836 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU D 841 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 842 " --> pdb=" O LEU D 838 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 843 " --> pdb=" O TYR D 839 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 847 " --> pdb=" O ILE D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 866 removed outlier: 3.537A pdb=" N ALA D 855 " --> pdb=" O GLU D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 885 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.875A pdb=" N ARG E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 149 Processing helix chain 'E' and resid 151 through 161 Processing helix chain 'E' and resid 170 through 184 removed outlier: 3.526A pdb=" N TYR E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 Processing helix chain 'E' and resid 205 through 220 Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 241 through 256 removed outlier: 3.906A pdb=" N CYS E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 removed outlier: 4.279A pdb=" N MET E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.573A pdb=" N LYS E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.621A pdb=" N LEU E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 326 Processing helix chain 'E' and resid 328 through 342 Processing helix chain 'E' and resid 346 through 361 removed outlier: 4.249A pdb=" N TYR E 350 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 375 removed outlier: 3.599A pdb=" N GLU E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 395 removed outlier: 3.796A pdb=" N GLY E 395 " --> pdb=" O VAL E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 412 removed outlier: 3.596A pdb=" N PHE E 405 " --> pdb=" O VAL E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 431 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.744A pdb=" N GLU E 460 " --> pdb=" O THR E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 480 Processing helix chain 'E' and resid 486 through 499 removed outlier: 3.524A pdb=" N PHE E 490 " --> pdb=" O MET E 486 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS E 495 " --> pdb=" O ASN E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 517 removed outlier: 3.615A pdb=" N GLU E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 517 " --> pdb=" O MET E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 535 removed outlier: 3.579A pdb=" N PHE E 525 " --> pdb=" O ASN E 521 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 551 removed outlier: 4.491A pdb=" N ILE E 542 " --> pdb=" O PHE E 538 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 543 " --> pdb=" O GLU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 567 removed outlier: 3.965A pdb=" N TYR E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 587 Processing helix chain 'E' and resid 591 through 605 removed outlier: 3.879A pdb=" N MET E 597 " --> pdb=" O ILE E 593 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 620 removed outlier: 3.584A pdb=" N VAL E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET E 619 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 630 removed outlier: 3.802A pdb=" N VAL E 629 " --> pdb=" O ASP E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 654 removed outlier: 4.212A pdb=" N TYR E 649 " --> pdb=" O GLN E 645 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL E 650 " --> pdb=" O MET E 646 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 654 " --> pdb=" O VAL E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'E' and resid 661 through 675 removed outlier: 3.658A pdb=" N TRP E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 683 Processing helix chain 'E' and resid 684 through 693 removed outlier: 4.090A pdb=" N GLU E 688 " --> pdb=" O ARG E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 732 removed outlier: 3.557A pdb=" N LEU E 732 " --> pdb=" O ASP E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 754 removed outlier: 3.905A pdb=" N LYS E 754 " --> pdb=" O GLN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 760 removed outlier: 3.792A pdb=" N THR E 758 " --> pdb=" O SER E 755 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG E 759 " --> pdb=" O SER E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 774 removed outlier: 3.573A pdb=" N ALA E 766 " --> pdb=" O PRO E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 793 through 801 removed outlier: 3.797A pdb=" N ILE E 799 " --> pdb=" O GLN E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 126 through 137 removed outlier: 3.779A pdb=" N SER F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.516A pdb=" N TYR F 144 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE F 149 " --> pdb=" O TYR F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 194 Processing helix chain 'F' and resid 195 through 201 removed outlier: 3.548A pdb=" N VAL F 201 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 212 removed outlier: 3.979A pdb=" N GLU F 209 " --> pdb=" O ASP F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 250 removed outlier: 5.931A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ARG F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.593A pdb=" N ARG F 316 " --> pdb=" O TRP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 404 through 426 removed outlier: 4.313A pdb=" N LYS F 408 " --> pdb=" O PRO F 404 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 removed outlier: 3.646A pdb=" N TYR F 430 " --> pdb=" O ASN F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 475 through 496 removed outlier: 3.935A pdb=" N ALA F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 481 " --> pdb=" O GLU F 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 488 " --> pdb=" O GLN F 484 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 489 " --> pdb=" O HIS F 485 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 540 removed outlier: 3.655A pdb=" N ARG F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 594 removed outlier: 3.715A pdb=" N SER F 593 " --> pdb=" O VAL F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 615 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.808A pdb=" N LYS G 95 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G 96 " --> pdb=" O GLN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 113 removed outlier: 3.658A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 136 Processing helix chain 'G' and resid 146 through 157 removed outlier: 3.521A pdb=" N GLN G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 216 through 221 removed outlier: 4.208A pdb=" N TYR G 220 " --> pdb=" O TRP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 Processing helix chain 'G' and resid 241 through 253 removed outlier: 3.509A pdb=" N ALA G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 232 through 236 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.685A pdb=" N VAL H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 280 through 290 removed outlier: 3.643A pdb=" N ALA H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 310 removed outlier: 3.629A pdb=" N LYS H 295 " --> pdb=" O ARG H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 316 Processing helix chain 'H' and resid 317 through 319 No H-bonds generated for 'chain 'H' and resid 317 through 319' Processing helix chain 'H' and resid 327 through 339 Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 354 through 362 Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 371 through 376 removed outlier: 3.538A pdb=" N ARG H 376 " --> pdb=" O PRO H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 383 Processing helix chain 'H' and resid 393 through 396 removed outlier: 3.514A pdb=" N ASN H 396 " --> pdb=" O PRO H 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 393 through 396' Processing helix chain 'H' and resid 418 through 426 removed outlier: 3.508A pdb=" N HIS H 426 " --> pdb=" O TYR H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 437 Processing helix chain 'H' and resid 438 through 446 Processing helix chain 'I' and resid 144 through 153 removed outlier: 3.563A pdb=" N GLU I 147 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS I 149 " --> pdb=" O SER I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 160 removed outlier: 3.946A pdb=" N ARG I 160 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.710A pdb=" N VAL I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 202 Processing helix chain 'I' and resid 238 through 242 Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 265 through 269 removed outlier: 3.682A pdb=" N SER I 269 " --> pdb=" O VAL I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 287 Processing helix chain 'I' and resid 297 through 302 removed outlier: 3.748A pdb=" N ARG I 302 " --> pdb=" O PRO I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 311 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'I' and resid 333 through 341 removed outlier: 4.092A pdb=" N TYR I 337 " --> pdb=" O ASP I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 405 through 409 removed outlier: 3.592A pdb=" N THR I 409 " --> pdb=" O VAL I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 433 Processing helix chain 'I' and resid 434 through 438 removed outlier: 3.947A pdb=" N TYR I 437 " --> pdb=" O PRO I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 457 removed outlier: 4.153A pdb=" N PHE I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 450 " --> pdb=" O GLN I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 481 Processing helix chain 'i' and resid 302 through 309 removed outlier: 3.738A pdb=" N ARG i 308 " --> pdb=" O GLU i 304 " (cutoff:3.500A) Processing helix chain 'i' and resid 326 through 338 Processing helix chain 'i' and resid 350 through 363 Processing helix chain 'i' and resid 410 through 417 removed outlier: 3.570A pdb=" N LEU i 414 " --> pdb=" O ASN i 410 " (cutoff:3.500A) Processing helix chain 'i' and resid 429 through 446 removed outlier: 3.677A pdb=" N LEU i 434 " --> pdb=" O PRO i 430 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR i 435 " --> pdb=" O ASN i 431 " (cutoff:3.500A) Processing helix chain 'i' and resid 457 through 462 removed outlier: 4.048A pdb=" N GLU i 462 " --> pdb=" O PRO i 459 " (cutoff:3.500A) Processing helix chain 'i' and resid 463 through 471 Processing helix chain 'i' and resid 485 through 492 Processing helix chain 'i' and resid 514 through 519 removed outlier: 3.995A pdb=" N ILE i 518 " --> pdb=" O PRO i 514 " (cutoff:3.500A) Processing helix chain 'i' and resid 565 through 582 removed outlier: 3.788A pdb=" N VAL i 581 " --> pdb=" O ARG i 577 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN i 582 " --> pdb=" O MET i 578 " (cutoff:3.500A) Processing helix chain 'i' and resid 583 through 586 removed outlier: 3.743A pdb=" N MET i 586 " --> pdb=" O PRO i 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 583 through 586' Processing helix chain 'i' and resid 588 through 614 Processing helix chain 'i' and resid 634 through 639 removed outlier: 3.508A pdb=" N GLU i 638 " --> pdb=" O LYS i 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 108 removed outlier: 4.198A pdb=" N TYR J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 150 No H-bonds generated for 'chain 'J' and resid 148 through 150' Processing helix chain 'J' and resid 171 through 178 removed outlier: 3.753A pdb=" N ILE J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 197 removed outlier: 3.586A pdb=" N LEU J 189 " --> pdb=" O SER J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 208 Processing helix chain 'J' and resid 224 through 231 Processing helix chain 'J' and resid 233 through 255 Processing helix chain 'J' and resid 260 through 265 Processing helix chain 'J' and resid 269 through 283 removed outlier: 3.987A pdb=" N PHE J 273 " --> pdb=" O ASP J 269 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE J 274 " --> pdb=" O PRO J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 360 removed outlier: 3.703A pdb=" N PHE J 356 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET J 357 " --> pdb=" O ASN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 389 removed outlier: 3.562A pdb=" N PHE J 389 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 423 removed outlier: 3.545A pdb=" N ILE J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 454 removed outlier: 3.835A pdb=" N LYS J 443 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU J 444 " --> pdb=" O LYS J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 470 removed outlier: 3.545A pdb=" N ASP J 463 " --> pdb=" O THR J 459 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP J 468 " --> pdb=" O GLN J 464 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET J 470 " --> pdb=" O ILE J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 505 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 231 through 233 No H-bonds generated for 'chain 'K' and resid 231 through 233' Processing helix chain 'K' and resid 298 through 321 removed outlier: 4.111A pdb=" N LYS K 321 " --> pdb=" O ARG K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 74 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.516A pdb=" N ASP L 90 " --> pdb=" O ASN L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 108 removed outlier: 3.610A pdb=" N LEU L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN L 108 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 132 removed outlier: 3.508A pdb=" N TRP L 129 " --> pdb=" O HIS L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 removed outlier: 4.052A pdb=" N GLN L 146 " --> pdb=" O GLY L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 169 removed outlier: 3.773A pdb=" N LYS L 160 " --> pdb=" O GLU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 235 Processing helix chain 'L' and resid 237 through 247 removed outlier: 3.548A pdb=" N TYR L 241 " --> pdb=" O ARG L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 282 removed outlier: 3.695A pdb=" N VAL L 255 " --> pdb=" O SER L 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 85 removed outlier: 3.563A pdb=" N GLN M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 118 removed outlier: 4.254A pdb=" N LEU M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET M 107 " --> pdb=" O PRO M 103 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN M 109 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 Processing helix chain 'M' and resid 166 through 177 Processing helix chain 'm' and resid 76 through 81 removed outlier: 3.736A pdb=" N ILE m 80 " --> pdb=" O SER m 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN m 81 " --> pdb=" O ALA m 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 76 through 81' Processing helix chain 'm' and resid 101 through 118 removed outlier: 4.015A pdb=" N ILE m 105 " --> pdb=" O CYS m 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU m 106 " --> pdb=" O GLY m 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN m 109 " --> pdb=" O ILE m 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU m 117 " --> pdb=" O MET m 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 138 removed outlier: 3.927A pdb=" N ARG m 137 " --> pdb=" O TYR m 133 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP m 138 " --> pdb=" O GLU m 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 166 through 177 Processing helix chain 'N' and resid 239 through 246 Processing helix chain 'N' and resid 286 through 298 Processing helix chain 'N' and resid 309 through 313 removed outlier: 3.590A pdb=" N GLU N 312 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 333 removed outlier: 4.412A pdb=" N ALA N 333 " --> pdb=" O LEU N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 345 Proline residue: N 340 - end of helix removed outlier: 3.716A pdb=" N THR N 345 " --> pdb=" O SER N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 370 removed outlier: 3.767A pdb=" N THR N 358 " --> pdb=" O GLY N 354 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 360 " --> pdb=" O THR N 356 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU N 361 " --> pdb=" O THR N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 411 removed outlier: 3.570A pdb=" N ASN N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 428 Processing helix chain 'N' and resid 447 through 452 Processing helix chain 'N' and resid 455 through 468 removed outlier: 3.723A pdb=" N MET N 468 " --> pdb=" O LEU N 464 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 491 removed outlier: 3.601A pdb=" N ALA N 486 " --> pdb=" O ASP N 482 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN N 491 " --> pdb=" O PHE N 487 " (cutoff:3.500A) Processing helix chain 'N' and resid 542 through 559 removed outlier: 3.713A pdb=" N ALA N 553 " --> pdb=" O LEU N 549 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 554 " --> pdb=" O ALA N 550 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL N 558 " --> pdb=" O VAL N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 564 removed outlier: 3.690A pdb=" N ASP N 564 " --> pdb=" O PRO N 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 561 through 564' Processing helix chain 'N' and resid 565 through 573 Processing helix chain 'N' and resid 597 through 612 Processing helix chain 'N' and resid 629 through 642 removed outlier: 3.950A pdb=" N ILE N 633 " --> pdb=" O GLY N 629 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS N 641 " --> pdb=" O ILE N 637 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 666 Processing helix chain 'N' and resid 667 through 669 No H-bonds generated for 'chain 'N' and resid 667 through 669' Processing helix chain 'N' and resid 671 through 680 Processing helix chain 'N' and resid 698 through 709 removed outlier: 3.852A pdb=" N ALA N 702 " --> pdb=" O ILE N 698 " (cutoff:3.500A) Processing helix chain 'N' and resid 738 through 756 removed outlier: 4.149A pdb=" N CYS N 742 " --> pdb=" O ASP N 738 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP N 750 " --> pdb=" O LEU N 746 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU N 751 " --> pdb=" O GLN N 747 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.574A pdb=" N VAL O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 80 removed outlier: 3.570A pdb=" N HIS O 77 " --> pdb=" O THR O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 104 removed outlier: 3.776A pdb=" N PHE O 89 " --> pdb=" O ASN O 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL O 90 " --> pdb=" O ARG O 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN O 103 " --> pdb=" O GLN O 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN O 104 " --> pdb=" O TYR O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 124 Processing helix chain 'O' and resid 130 through 134 Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'P' and resid 57 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 24 removed outlier: 9.298A pdb=" N TRP A 15 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER A 35 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N CYS A 17 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE A 33 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 19 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 23 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR A 29 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A 205 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG A 31 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 203 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE A 33 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU A 201 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER A 35 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A 199 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN A 196 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER A 188 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 198 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 186 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 200 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 184 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU A 202 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 182 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP A 204 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 110 removed outlier: 3.831A pdb=" N PHE A 145 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 64 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU A 152 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE A 62 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN A 154 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR A 60 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 118 removed outlier: 7.464A pdb=" N SER A 115 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER A 138 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 117 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 15 through 24 removed outlier: 9.206A pdb=" N TRP a 15 " --> pdb=" O SER a 35 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER a 35 " --> pdb=" O TRP a 15 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS a 17 " --> pdb=" O ILE a 33 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE a 33 " --> pdb=" O CYS a 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU a 19 " --> pdb=" O ARG a 31 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU a 27 " --> pdb=" O ASP a 23 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU a 197 " --> pdb=" O PRO a 36 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN a 181 " --> pdb=" O TRP a 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 121 through 122 removed outlier: 3.644A pdb=" N SER a 107 " --> pdb=" O ILE a 122 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG a 64 " --> pdb=" O GLN a 150 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU a 152 " --> pdb=" O ILE a 62 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE a 62 " --> pdb=" O GLU a 152 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN a 154 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR a 60 " --> pdb=" O ASN a 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 96 through 97 Processing sheet with id=AA8, first strand: chain 'a' and resid 114 through 117 removed outlier: 3.654A pdb=" N ALA a 137 " --> pdb=" O VAL a 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 156 through 157 removed outlier: 3.651A pdb=" N GLY a 156 " --> pdb=" O PHE a 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 60 removed outlier: 4.104A pdb=" N GLY B 102 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 82 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE B 100 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB3, first strand: chain 'B' and resid 312 through 315 removed outlier: 3.622A pdb=" N ASN B 124 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'B' and resid 135 through 137 Processing sheet with id=AB6, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.762A pdb=" N TRP B 169 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 443 through 444 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 466 through 469 current: chain 'B' and resid 496 through 501 Processing sheet with id=AB8, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB9, first strand: chain 'B' and resid 579 through 580 removed outlier: 6.859A pdb=" N ALA B 579 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 602 through 607 removed outlier: 7.229A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR B 590 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 596 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 610 through 613 Processing sheet with id=AC3, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AC4, first strand: chain 'B' and resid 652 through 654 removed outlier: 7.812A pdb=" N VAL B 671 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 833 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 673 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 658 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B 941 " --> pdb=" O TYR B 659 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 685 through 691 removed outlier: 3.537A pdb=" N SER B 685 " --> pdb=" O ARG B 812 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP B 787 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 809 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 785 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1052 through 1054 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1052 through 1054 current: chain 'B' and resid 1065 through 1066 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1065 through 1066 current: chain 'c' and resid 1306 through 1308 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 112 through 121 removed outlier: 10.180A pdb=" N LEU C 116 " --> pdb=" O PRO C 277 " (cutoff:3.500A) removed outlier: 10.755A pdb=" N CYS C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 275 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 120 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AC9, first strand: chain 'C' and resid 391 through 393 Processing sheet with id=AD1, first strand: chain 'C' and resid 401 through 405 Processing sheet with id=AD2, first strand: chain 'C' and resid 610 through 614 removed outlier: 4.201A pdb=" N ILE C 658 " --> pdb=" O TRP C 614 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 629 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL K 263 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE H 193 " --> pdb=" O VAL K 264 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 226 through 228 removed outlier: 3.711A pdb=" N ILE c 283 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL c 248 " --> pdb=" O ARG c 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 253 through 255 removed outlier: 7.013A pdb=" N ILE c 253 " --> pdb=" O ILE c 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 351 through 353 removed outlier: 6.750A pdb=" N VAL c 352 " --> pdb=" O ILE c 420 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 388 through 390 removed outlier: 3.734A pdb=" N GLN c 412 " --> pdb=" O ILE c 360 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 436 through 441 removed outlier: 4.186A pdb=" N VAL c1130 " --> pdb=" O ILE c 440 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU c1129 " --> pdb=" O HIS c1116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR c1114 " --> pdb=" O THR c1131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 1104 through 1109 removed outlier: 3.626A pdb=" N SER c 472 " --> pdb=" O ALA c1109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 480 through 483 Processing sheet with id=AE1, first strand: chain 'c' and resid 497 through 498 removed outlier: 6.655A pdb=" N GLN c 497 " --> pdb=" O HIS F 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 570 through 571 removed outlier: 3.601A pdb=" N PHE c 867 " --> pdb=" O VAL c 856 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 596 through 597 removed outlier: 5.724A pdb=" N ILE c 610 " --> pdb=" O LEU c 837 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU c 837 " --> pdb=" O ILE c 610 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU c 806 " --> pdb=" O ALA F 605 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA F 605 " --> pdb=" O LEU c 806 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE c 808 " --> pdb=" O GLU F 603 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU F 603 " --> pdb=" O ILE c 808 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN c 810 " --> pdb=" O TRP F 601 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 662 through 664 Processing sheet with id=AE5, first strand: chain 'c' and resid 669 through 674 removed outlier: 3.691A pdb=" N SER c 685 " --> pdb=" O VAL c 705 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 722 through 724 removed outlier: 3.510A pdb=" N ASP c 722 " --> pdb=" O VAL c 775 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 948 through 951 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 948 through 951 current: chain 'c' and resid 1034 through 1035 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 1034 through 1035 current: chain 'c' and resid 1099 through 1102 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 1099 through 1102 current: chain 'F' and resid 292 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 303 through 306 current: chain 'F' and resid 342 through 346 Processing sheet with id=AE8, first strand: chain 'c' and resid 999 through 1000 removed outlier: 4.470A pdb=" N MET F 162 " --> pdb=" O HIS c1000 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 1044 through 1045 Processing sheet with id=AF1, first strand: chain 'c' and resid 1248 through 1250 Processing sheet with id=AF2, first strand: chain 'E' and resid 700 through 701 removed outlier: 6.738A pdb=" N TRP E 706 " --> pdb=" O SER E 744 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL E 746 " --> pdb=" O TRP E 706 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 708 " --> pdb=" O VAL E 746 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 190 through 195 removed outlier: 3.660A pdb=" N ARG G 190 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE G 180 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY G 212 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 182 " --> pdb=" O LEU G 210 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 216 through 217 removed outlier: 3.512A pdb=" N HIS H 216 " --> pdb=" O TRP K 330 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 179 through 183 removed outlier: 6.344A pdb=" N VAL I 119 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET I 183 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS I 121 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU I 118 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N HIS I 261 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE I 120 " --> pdb=" O HIS I 261 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ASN I 263 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE I 122 " --> pdb=" O ASN I 263 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE I 260 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP I 293 " --> pdb=" O PHE I 260 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE I 262 " --> pdb=" O ASP I 293 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AF7, first strand: chain 'I' and resid 233 through 236 removed outlier: 6.921A pdb=" N HIS I 221 " --> pdb=" O LYS I 235 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR M 146 " --> pdb=" O PHE M 96 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS M 73 " --> pdb=" O LYS M 126 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP M 128 " --> pdb=" O LYS M 73 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 341 through 344 removed outlier: 4.385A pdb=" N ASN i 423 " --> pdb=" O PHE i 283 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE i 420 " --> pdb=" O PHE i 451 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP i 453 " --> pdb=" O PHE i 420 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE i 422 " --> pdb=" O ASP i 453 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 295 through 296 Processing sheet with id=AG1, first strand: chain 'i' and resid 346 through 348 Processing sheet with id=AG2, first strand: chain 'i' and resid 393 through 397 removed outlier: 4.402A pdb=" N THR i 395 " --> pdb=" O HIS i 382 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N HIS i 382 " --> pdb=" O THR i 395 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS i 397 " --> pdb=" O ILE i 380 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE i 380 " --> pdb=" O LYS i 397 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR m 146 " --> pdb=" O PHE m 96 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE m 93 " --> pdb=" O VAL m 125 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL m 127 " --> pdb=" O ILE m 93 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP m 95 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS m 73 " --> pdb=" O LYS m 126 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASP m 128 " --> pdb=" O LYS m 73 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 96 through 97 removed outlier: 3.576A pdb=" N GLU J 96 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 112 through 113 removed outlier: 6.358A pdb=" N VAL J 141 " --> pdb=" O ILE J 331 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE J 331 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET J 143 " --> pdb=" O VAL J 329 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 151 through 154 Processing sheet with id=AG6, first strand: chain 'J' and resid 309 through 310 removed outlier: 5.976A pdb=" N ASN J 309 " --> pdb=" O VAL J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'J' and resid 380 through 381 removed outlier: 6.373A pdb=" N ILE J 380 " --> pdb=" O TRP J 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'J' and resid 391 through 392 removed outlier: 3.656A pdb=" N TYR J 399 " --> pdb=" O SER J 392 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 138 through 142 removed outlier: 3.715A pdb=" N ARG K 151 " --> pdb=" O GLU K 165 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU K 165 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE K 190 " --> pdb=" O TYR K 161 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG K 191 " --> pdb=" O HIS K 229 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N SER K 222 " --> pdb=" O VAL K 249 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N VAL K 249 " --> pdb=" O SER K 222 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N VAL K 224 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ILE K 247 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N LEU K 226 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLU K 245 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS K 228 " --> pdb=" O ASP K 243 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER K 256 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG K 180 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ARG K 259 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 201 through 203 Processing sheet with id=AH2, first strand: chain 'L' and resid 201 through 207 removed outlier: 7.074A pdb=" N GLY L 173 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP L 224 " --> pdb=" O GLY L 173 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA L 175 " --> pdb=" O THR L 222 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR L 222 " --> pdb=" O ALA L 175 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU L 177 " --> pdb=" O LEU L 220 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 347 through 349 Processing sheet with id=AH4, first strand: chain 'N' and resid 589 through 592 removed outlier: 6.369A pdb=" N GLY N 589 " --> pdb=" O VAL N 716 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL N 718 " --> pdb=" O GLY N 589 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE N 591 " --> pdb=" O VAL N 718 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE N 617 " --> pdb=" O VAL N 717 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL N 616 " --> pdb=" O VAL N 644 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE N 646 " --> pdb=" O VAL N 616 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR N 618 " --> pdb=" O ILE N 646 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR N 648 " --> pdb=" O THR N 618 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE N 620 " --> pdb=" O THR N 648 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP N 650 " --> pdb=" O PHE N 620 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N CYS N 622 " --> pdb=" O ASP N 650 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR N 645 " --> pdb=" O PHE N 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'N' and resid 727 through 729 removed outlier: 4.012A pdb=" N LYS N 732 " --> pdb=" O GLU N 729 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 51 through 54 removed outlier: 3.643A pdb=" N ARG P 51 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP P 113 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU P 88 " --> pdb=" O SER P 136 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP P 72 " --> pdb=" O GLU P 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 78 through 82 removed outlier: 3.593A pdb=" N ALA P 123 " --> pdb=" O TRP P 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL P 96 " --> pdb=" O PHE P 109 " (cutoff:3.500A) 2645 hydrogen bonds defined for protein. 7542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.08 Time building geometry restraints manager: 22.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10512 1.31 - 1.44: 15983 1.44 - 1.56: 34814 1.56 - 1.69: 0 1.69 - 1.81: 431 Bond restraints: 61740 Sorted by residual: bond pdb=" C CYS D 249 " pdb=" O CYS D 249 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.17e-02 7.31e+03 4.26e+01 bond pdb=" CA PHE L 155 " pdb=" C PHE L 155 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.30e-02 5.92e+03 2.98e+01 bond pdb=" CA TYR B 76 " pdb=" C TYR B 76 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.23e-02 6.61e+03 2.81e+01 bond pdb=" CA SER B 77 " pdb=" C SER B 77 " ideal model delta sigma weight residual 1.522 1.460 0.062 1.20e-02 6.94e+03 2.66e+01 bond pdb=" CA TYR J 399 " pdb=" C TYR J 399 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.24e-02 6.50e+03 2.55e+01 ... (remaining 61735 not shown) Histogram of bond angle deviations from ideal: 92.30 - 100.86: 85 100.86 - 109.42: 5564 109.42 - 117.98: 40531 117.98 - 126.54: 36860 126.54 - 135.10: 937 Bond angle restraints: 83977 Sorted by residual: angle pdb=" N PHE L 152 " pdb=" CA PHE L 152 " pdb=" C PHE L 152 " ideal model delta sigma weight residual 109.52 92.30 17.22 1.55e+00 4.16e-01 1.23e+02 angle pdb=" N ASP E 364 " pdb=" CA ASP E 364 " pdb=" C ASP E 364 " ideal model delta sigma weight residual 114.31 100.96 13.35 1.29e+00 6.01e-01 1.07e+02 angle pdb=" N GLN E 365 " pdb=" CA GLN E 365 " pdb=" C GLN E 365 " ideal model delta sigma weight residual 111.36 100.30 11.06 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N PRO L 114 " pdb=" CA PRO L 114 " pdb=" C PRO L 114 " ideal model delta sigma weight residual 110.70 122.77 -12.07 1.22e+00 6.72e-01 9.78e+01 angle pdb=" N PRO c 401 " pdb=" CA PRO c 401 " pdb=" C PRO c 401 " ideal model delta sigma weight residual 110.70 122.58 -11.88 1.22e+00 6.72e-01 9.49e+01 ... (remaining 83972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 35280 17.48 - 34.96: 1362 34.96 - 52.44: 215 52.44 - 69.92: 38 69.92 - 87.40: 15 Dihedral angle restraints: 36910 sinusoidal: 13046 harmonic: 23864 Sorted by residual: dihedral pdb=" CB CYS m 101 " pdb=" SG CYS m 101 " pdb=" SG CYS m 104 " pdb=" CB CYS m 104 " ideal model delta sinusoidal sigma weight residual -86.00 -168.07 82.07 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" C VAL J 412 " pdb=" N VAL J 412 " pdb=" CA VAL J 412 " pdb=" CB VAL J 412 " ideal model delta harmonic sigma weight residual -122.00 -138.14 16.14 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" N VAL J 412 " pdb=" C VAL J 412 " pdb=" CA VAL J 412 " pdb=" CB VAL J 412 " ideal model delta harmonic sigma weight residual 123.40 136.04 -12.64 0 2.50e+00 1.60e-01 2.55e+01 ... (remaining 36907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 9235 0.136 - 0.271: 195 0.271 - 0.407: 37 0.407 - 0.542: 7 0.542 - 0.678: 1 Chirality restraints: 9475 Sorted by residual: chirality pdb=" CA LEU M 144 " pdb=" N LEU M 144 " pdb=" C LEU M 144 " pdb=" CB LEU M 144 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA LEU m 144 " pdb=" N LEU m 144 " pdb=" C LEU m 144 " pdb=" CB LEU m 144 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA VAL J 412 " pdb=" N VAL J 412 " pdb=" C VAL J 412 " pdb=" CB VAL J 412 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.12e+00 ... (remaining 9472 not shown) Planarity restraints: 11055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 133 " 0.027 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C LYS L 133 " -0.087 2.00e-02 2.50e+03 pdb=" O LYS L 133 " 0.031 2.00e-02 2.50e+03 pdb=" N PRO L 134 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 564 " -0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO F 565 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO F 565 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 565 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 252 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C SER D 252 " -0.054 2.00e-02 2.50e+03 pdb=" O SER D 252 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL D 253 " 0.018 2.00e-02 2.50e+03 ... (remaining 11052 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 55 2.33 - 2.97: 28482 2.97 - 3.62: 86659 3.62 - 4.26: 132213 4.26 - 4.90: 218757 Nonbonded interactions: 466166 Sorted by model distance: nonbonded pdb=" OD2 ASP L 224 " pdb="FE FE L2001 " model vdw 1.688 2.260 nonbonded pdb=" NE2 HIS L 73 " pdb="FE FE L2001 " model vdw 1.950 2.340 nonbonded pdb=" OE2 GLU B 889 " pdb="ZN ZN B1101 " model vdw 1.988 2.230 nonbonded pdb=" OE1 GLU B 535 " pdb="ZN ZN B1101 " model vdw 1.997 2.230 nonbonded pdb=" OD2 ASP G 214 " pdb="FE FE G2001 " model vdw 2.001 2.260 ... (remaining 466161 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 11 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 108 or (resid 109 and (name N or n \ ame CA or name C or name O or name CB )) or resid 110 or (resid 111 and (name N \ or name CA or name C or name O or name CB )) or resid 112 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 or (re \ sid 146 through 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 through 192 or (resid 193 and (name N or name CA or name C or name O o \ r name CB )) or resid 194 through 233 or (resid 234 through 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 262 through 277 or (resid 278 \ and (name N or name CA or name C or name O or name CB )) or resid 279 through 30 \ 2 or (resid 303 through 304 and (name N or name CA or name C or name O or name C \ B )) or resid 305 through 311 or (resid 312 through 313 and (name N or name CA o \ r name C or name O or name CB )) or resid 314 or (resid 315 and (name N or name \ CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 and \ (name N or name CA or name C or name O or name CB )) or resid 319 through 327)) selection = (chain 'a' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 23 or (resid 24 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 69 or (resid 70 through 78 and (n \ ame N or name CA or name C or name O or name CB )) or resid 79 through 81 or (re \ sid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 thro \ ugh 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) o \ r resid 134 through 137 or (resid 138 through 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 156 or (resid 157 through 167 an \ d (name N or name CA or name C or name O or name CB )) or resid 168 through 232 \ or (resid 233 through 235 and (name N or name CA or name C or name O or name CB \ )) or (resid 262 through 266 and (name N or name CA or name C or name O or name \ CB )) or resid 267 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 310 or (resid 311 thr \ ough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 t \ hrough 327)) } ncs_group { reference = (chain 'M' and ((resid 69 through 70 and (name N or name CA or name C or name O \ or name CB )) or resid 71 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 152 or (resid 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 or (resid 155 \ through 156 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 7 through 177)) selection = (chain 'm' and (resid 69 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 177)) } 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.050 Extract box with map and model: 14.970 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 136.330 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.005 0.090 61740 Z= 0.350 Angle : 0.720 17.222 83977 Z= 0.480 Chirality : 0.056 0.678 9475 Planarity : 0.004 0.097 11055 Dihedral : 9.632 87.402 21494 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.56 % Rotamer: Outliers : 1.71 % Allowed : 5.21 % Favored : 93.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.08), residues: 8157 helix: -0.41 (0.08), residues: 3256 sheet: -1.21 (0.16), residues: 989 loop : -2.11 (0.09), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 238 HIS 0.009 0.001 HIS J 400 PHE 0.027 0.001 PHE J 118 TYR 0.033 0.001 TYR J 399 ARG 0.005 0.000 ARG c 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 676 time to evaluate : 5.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8309 (m) cc_final: 0.7834 (p) REVERT: A 81 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 312 PHE cc_start: 0.8646 (t80) cc_final: 0.8421 (t80) REVERT: B 126 ILE cc_start: 0.9414 (mt) cc_final: 0.9178 (tt) REVERT: B 280 PHE cc_start: 0.8349 (m-10) cc_final: 0.8062 (t80) REVERT: B 730 SER cc_start: 0.8965 (t) cc_final: 0.8601 (m) REVERT: C 111 MET cc_start: 0.7239 (mtp) cc_final: 0.6996 (mtp) REVERT: C 446 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8262 (tm-30) REVERT: c 102 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: c 115 MET cc_start: 0.8865 (ttp) cc_final: 0.8619 (ttm) REVERT: c 383 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8592 (pp) REVERT: c 1163 MET cc_start: 0.8488 (mpp) cc_final: 0.8229 (mpp) REVERT: D 78 MET cc_start: 0.8724 (mmt) cc_final: 0.8251 (mmm) REVERT: E 634 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6202 (tt) REVERT: E 663 MET cc_start: 0.8907 (mtp) cc_final: 0.8668 (mmp) REVERT: F 226 MET cc_start: 0.9381 (ttm) cc_final: 0.9097 (ttt) REVERT: F 590 HIS cc_start: 0.8897 (m-70) cc_final: 0.8662 (m-70) REVERT: G 135 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: I 200 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9085 (m110) REVERT: i 432 MET cc_start: 0.9107 (tpt) cc_final: 0.8641 (tpp) REVERT: i 587 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (m) REVERT: i 631 HIS cc_start: 0.5961 (t-170) cc_final: 0.4927 (t-90) REVERT: K 253 LYS cc_start: 0.8848 (tptp) cc_final: 0.8636 (tppt) REVERT: K 283 ASP cc_start: 0.7578 (t0) cc_final: 0.7302 (t0) REVERT: K 298 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (p0) REVERT: M 79 ASP cc_start: 0.9015 (m-30) cc_final: 0.8698 (m-30) REVERT: M 172 ASP cc_start: 0.8480 (m-30) cc_final: 0.8206 (m-30) REVERT: m 76 SER cc_start: 0.9218 (m) cc_final: 0.8862 (t) REVERT: m 95 ASP cc_start: 0.8636 (t0) cc_final: 0.8424 (t0) REVERT: m 120 SER cc_start: 0.9331 (p) cc_final: 0.9118 (p) REVERT: m 139 MET cc_start: 0.9171 (tpp) cc_final: 0.8313 (tpp) REVERT: N 672 MET cc_start: 0.8665 (mtp) cc_final: 0.8253 (mtp) REVERT: O 128 TYR cc_start: 0.8538 (t80) cc_final: 0.8246 (t80) REVERT: P 46 GLU cc_start: 0.8044 (pp20) cc_final: 0.7717 (pm20) REVERT: P 122 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8422 (mt-10) outliers start: 95 outliers final: 17 residues processed: 767 average time/residue: 1.3722 time to fit residues: 1346.0449 Evaluate side-chains 387 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 363 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 383 ILE Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain I residue 200 ASN Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 587 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 687 optimal weight: 0.0170 chunk 616 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 416 optimal weight: 40.0000 chunk 329 optimal weight: 30.0000 chunk 638 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 387 optimal weight: 6.9990 chunk 474 optimal weight: 9.9990 chunk 739 optimal weight: 7.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 150 GLN A 196 GLN ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 285 ASN a 41 GLN a 150 GLN a 187 HIS a 191 ASN a 196 GLN a 221 ASN a 231 HIS B 58 GLN B 124 ASN B 128 GLN B 276 GLN B 278 ASN B 322 GLN B 372 HIS B 386 GLN B 503 GLN B 522 GLN B 551 GLN B 600 ASN B 621 HIS B 622 GLN B 625 GLN B 636 GLN B 666 ASN B 687 HIS B 881 HIS B 910 GLN B 938 GLN C 110 GLN C 209 GLN C 300 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 453 GLN C 455 HIS C 460 ASN C 471 GLN C 474 GLN C 505 HIS C 513 GLN C 560 ASN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS c 73 GLN c 77 GLN c 90 ASN ** c 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 145 GLN ** c 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 449 HIS c 497 GLN c 924 GLN c1001 ASN c1019 GLN ** c1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1051 ASN c1095 GLN c1151 GLN c1196 GLN c1207 GLN D 175 GLN D 420 GLN D 882 GLN E 464 GLN ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 GLN E 612 HIS ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 GLN F 81 ASN F 148 GLN F 196 HIS F 251 GLN F 278 GLN F 288 HIS F 317 HIS F 318 HIS ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN F 518 HIS F 591 ASN G 92 GLN G 226 ASN G 253 GLN H 195 GLN H 216 HIS H 247 GLN H 271 GLN H 300 GLN H 332 GLN H 399 GLN I 139 GLN I 173 HIS I 193 GLN I 200 ASN I 317 GLN I 346 GLN I 440 GLN i 361 ASN i 607 GLN J 243 GLN J 244 GLN J 254 ASN J 296 GLN J 373 HIS J 381 HIS J 496 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 313 GLN L 64 HIS L 208 ASN N 691 HIS O 120 ASN P 104 GLN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 61740 Z= 0.248 Angle : 0.543 11.221 83977 Z= 0.279 Chirality : 0.043 0.156 9475 Planarity : 0.004 0.068 11055 Dihedral : 4.211 145.558 8901 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.46 % Favored : 96.53 % Rotamer: Outliers : 2.50 % Allowed : 11.08 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.09), residues: 8157 helix: 0.68 (0.09), residues: 3298 sheet: -0.64 (0.16), residues: 983 loop : -1.68 (0.09), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 486 HIS 0.008 0.001 HIS a 187 PHE 0.016 0.001 PHE D 73 TYR 0.018 0.001 TYR M 65 ARG 0.011 0.001 ARG c 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 380 time to evaluate : 5.718 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: A 12 THR cc_start: 0.8354 (m) cc_final: 0.8078 (p) REVERT: A 56 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 81 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 307 MET cc_start: 0.9431 (mmm) cc_final: 0.9220 (mmm) REVERT: A 312 PHE cc_start: 0.8469 (t80) cc_final: 0.8135 (t80) REVERT: a 158 LEU cc_start: 0.9052 (tp) cc_final: 0.8353 (tt) REVERT: a 173 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7579 (t0) REVERT: a 197 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 107 MET cc_start: 0.8696 (ttm) cc_final: 0.8444 (ttp) REVERT: B 251 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: B 280 PHE cc_start: 0.8409 (m-10) cc_final: 0.7992 (t80) REVERT: B 727 MET cc_start: 0.7705 (ptp) cc_final: 0.7292 (ptp) REVERT: B 730 SER cc_start: 0.9036 (t) cc_final: 0.8657 (m) REVERT: C 111 MET cc_start: 0.7376 (mtp) cc_final: 0.7163 (mtp) REVERT: C 446 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8278 (tm-30) REVERT: c 32 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: c 316 GLU cc_start: 0.8421 (tt0) cc_final: 0.8132 (mt-10) REVERT: c 447 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7705 (mt-10) REVERT: c 1163 MET cc_start: 0.8488 (mpp) cc_final: 0.8236 (mpp) REVERT: E 513 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4404 (mmt) REVERT: E 633 MET cc_start: 0.8469 (mtt) cc_final: 0.8260 (mpt) REVERT: E 634 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6153 (tp) REVERT: E 663 MET cc_start: 0.8931 (mtp) cc_final: 0.8637 (mmp) REVERT: E 713 MET cc_start: 0.4945 (mpt) cc_final: 0.2992 (tpp) REVERT: F 211 MET cc_start: 0.8632 (mtm) cc_final: 0.8422 (mtm) REVERT: F 226 MET cc_start: 0.9208 (ttm) cc_final: 0.8928 (ttt) REVERT: F 590 HIS cc_start: 0.8757 (m-70) cc_final: 0.8553 (m-70) REVERT: G 98 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9164 (mm) REVERT: G 104 MET cc_start: 0.8347 (tpp) cc_final: 0.8029 (tpp) REVERT: G 150 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9076 (mt) REVERT: G 227 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7846 (p0) REVERT: i 432 MET cc_start: 0.9203 (tpt) cc_final: 0.8738 (tpp) REVERT: i 586 MET cc_start: 0.8445 (mtp) cc_final: 0.8197 (mtm) REVERT: i 606 ASP cc_start: 0.8313 (t0) cc_final: 0.7949 (t0) REVERT: i 622 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8025 (mpt) REVERT: i 630 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: i 631 HIS cc_start: 0.5092 (t-170) cc_final: 0.4796 (t-90) REVERT: J 308 MET cc_start: 0.9194 (mmm) cc_final: 0.8981 (mmm) REVERT: K 253 LYS cc_start: 0.8879 (tptp) cc_final: 0.8668 (tppt) REVERT: K 283 ASP cc_start: 0.7681 (t0) cc_final: 0.7369 (t0) REVERT: K 298 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6804 (p0) REVERT: L 144 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.4037 (mp) REVERT: M 69 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: m 139 MET cc_start: 0.9079 (tpp) cc_final: 0.8208 (tpp) REVERT: N 664 MET cc_start: 0.8373 (mmt) cc_final: 0.8033 (mmm) REVERT: N 672 MET cc_start: 0.8580 (mtp) cc_final: 0.8158 (mtp) REVERT: N 674 ASP cc_start: 0.9267 (t0) cc_final: 0.8392 (t0) REVERT: O 102 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8550 (tm-30) REVERT: O 104 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7490 (p0) REVERT: P 71 MET cc_start: 0.9091 (tpt) cc_final: 0.8381 (tpt) REVERT: P 107 MET cc_start: 0.8417 (ptp) cc_final: 0.8211 (ptp) outliers start: 139 outliers final: 43 residues processed: 490 average time/residue: 1.2255 time to fit residues: 796.0315 Evaluate side-chains 397 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 339 time to evaluate : 5.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 173 ASP Chi-restraints excluded: chain a residue 217 GLU Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain c residue 32 MET Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 448 MET Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain i residue 454 VAL Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 622 MET Chi-restraints excluded: chain i residue 630 ASP Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain K residue 172 ASP Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 410 optimal weight: 50.0000 chunk 229 optimal weight: 0.0270 chunk 615 optimal weight: 4.9990 chunk 503 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 740 optimal weight: 10.0000 chunk 799 optimal weight: 1.9990 chunk 659 optimal weight: 5.9990 chunk 734 optimal weight: 0.0070 chunk 252 optimal weight: 10.0000 chunk 594 optimal weight: 3.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN B 865 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c1042 ASN D 468 ASN ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 HIS ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN H 343 ASN I 346 GLN J 288 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 61740 Z= 0.239 Angle : 0.513 10.170 83977 Z= 0.262 Chirality : 0.042 0.175 9475 Planarity : 0.004 0.050 11055 Dihedral : 3.718 50.546 8880 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.70 % Allowed : 11.53 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 8157 helix: 1.13 (0.09), residues: 3319 sheet: -0.53 (0.16), residues: 991 loop : -1.42 (0.09), residues: 3847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.014 0.001 PHE c 278 TYR 0.015 0.001 TYR i 641 ARG 0.007 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 356 time to evaluate : 6.059 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: A 12 THR cc_start: 0.8503 (m) cc_final: 0.8220 (p) REVERT: A 56 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: A 81 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 312 PHE cc_start: 0.8575 (t80) cc_final: 0.8224 (t80) REVERT: a 107 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8905 (p) REVERT: a 289 MET cc_start: 0.9273 (mtp) cc_final: 0.9027 (mtt) REVERT: B 251 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5582 (m-80) REVERT: B 280 PHE cc_start: 0.8378 (m-10) cc_final: 0.8046 (t80) REVERT: B 544 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: B 727 MET cc_start: 0.7741 (ptp) cc_final: 0.7363 (ptp) REVERT: B 730 SER cc_start: 0.9037 (t) cc_final: 0.8697 (m) REVERT: C 124 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6471 (p-90) REVERT: C 446 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8276 (tm-30) REVERT: c 102 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: c 447 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7659 (mt-10) REVERT: c 988 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9115 (pp) REVERT: c 1163 MET cc_start: 0.8473 (mpp) cc_final: 0.8222 (mpp) REVERT: E 513 MET cc_start: 0.4730 (OUTLIER) cc_final: 0.4336 (mmt) REVERT: E 634 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5664 (tp) REVERT: E 654 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4328 (pp) REVERT: E 663 MET cc_start: 0.8924 (mtp) cc_final: 0.8633 (mmp) REVERT: E 713 MET cc_start: 0.4868 (mpt) cc_final: 0.2753 (tpp) REVERT: F 590 HIS cc_start: 0.8814 (m-70) cc_final: 0.8575 (m-70) REVERT: G 104 MET cc_start: 0.8334 (tpp) cc_final: 0.8001 (tpp) REVERT: G 150 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9105 (mt) REVERT: G 227 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7847 (p0) REVERT: I 485 MET cc_start: 0.8694 (mmm) cc_final: 0.8088 (mtt) REVERT: i 432 MET cc_start: 0.9196 (tpt) cc_final: 0.8739 (tpp) REVERT: i 586 MET cc_start: 0.8473 (mtp) cc_final: 0.8228 (mtm) REVERT: i 606 ASP cc_start: 0.8380 (t0) cc_final: 0.7971 (t0) REVERT: K 283 ASP cc_start: 0.7612 (t0) cc_final: 0.7290 (t0) REVERT: L 158 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6226 (t80) REVERT: m 95 ASP cc_start: 0.8797 (t0) cc_final: 0.8555 (t0) REVERT: m 139 MET cc_start: 0.8936 (tpp) cc_final: 0.8216 (tpp) REVERT: N 664 MET cc_start: 0.8621 (mmt) cc_final: 0.8248 (mmm) REVERT: N 672 MET cc_start: 0.8571 (mtp) cc_final: 0.8106 (mtp) REVERT: O 67 ASP cc_start: 0.8108 (t0) cc_final: 0.7814 (m-30) REVERT: O 84 ASP cc_start: 0.8584 (t0) cc_final: 0.8266 (t0) REVERT: O 102 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8557 (tm-30) REVERT: P 107 MET cc_start: 0.8437 (ptp) cc_final: 0.8177 (ptp) outliers start: 150 outliers final: 46 residues processed: 467 average time/residue: 1.2032 time to fit residues: 750.0428 Evaluate side-chains 388 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 5.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 427 MET Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 121 ASN Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 731 optimal weight: 8.9990 chunk 556 optimal weight: 0.8980 chunk 384 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 743 optimal weight: 50.0000 chunk 786 optimal weight: 8.9990 chunk 388 optimal weight: 0.8980 chunk 704 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 181 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 ASN B1000 HIS ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 GLN ** c 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c1076 ASN c1315 ASN D 227 ASN ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 ASN ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 486 HIS ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN m 81 GLN O 120 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 61740 Z= 0.404 Angle : 0.594 10.931 83977 Z= 0.303 Chirality : 0.044 0.191 9475 Planarity : 0.004 0.073 11055 Dihedral : 3.955 51.313 8874 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.67 % Allowed : 12.51 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 8157 helix: 1.32 (0.09), residues: 3297 sheet: -0.47 (0.16), residues: 1011 loop : -1.32 (0.10), residues: 3849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.022 0.001 PHE B 867 TYR 0.023 0.002 TYR i 560 ARG 0.010 0.001 ARG F 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 335 time to evaluate : 5.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 THR cc_start: 0.8616 (m) cc_final: 0.8296 (p) REVERT: A 56 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 81 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 307 MET cc_start: 0.9405 (mmm) cc_final: 0.9057 (mmt) REVERT: a 289 MET cc_start: 0.9236 (mtp) cc_final: 0.8996 (mtt) REVERT: a 307 MET cc_start: 0.9299 (mmm) cc_final: 0.9029 (mmm) REVERT: B 251 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: B 280 PHE cc_start: 0.8340 (m-10) cc_final: 0.7915 (t80) REVERT: B 730 SER cc_start: 0.9125 (t) cc_final: 0.8865 (p) REVERT: C 124 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.6637 (p-90) REVERT: C 446 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8253 (tm-30) REVERT: c 153 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7337 (ppp) REVERT: c 255 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7848 (mtt) REVERT: c 313 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: c 447 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7775 (mt-10) REVERT: c 988 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9140 (pp) REVERT: c 1028 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: c 1163 MET cc_start: 0.8480 (mpp) cc_final: 0.8269 (mpp) REVERT: D 96 MET cc_start: 0.8029 (tpt) cc_final: 0.7817 (mmm) REVERT: D 125 MET cc_start: 0.9403 (ttp) cc_final: 0.8773 (tpt) REVERT: E 486 MET cc_start: 0.8221 (pmm) cc_final: 0.7826 (pmm) REVERT: E 513 MET cc_start: 0.4933 (OUTLIER) cc_final: 0.4544 (mmt) REVERT: E 633 MET cc_start: 0.7340 (mpt) cc_final: 0.7025 (mmt) REVERT: E 634 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5772 (tp) REVERT: E 646 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4649 (ppp) REVERT: E 663 MET cc_start: 0.8958 (mtp) cc_final: 0.8629 (mmp) REVERT: E 713 MET cc_start: 0.4689 (mpt) cc_final: 0.2561 (tpp) REVERT: F 590 HIS cc_start: 0.8887 (m-70) cc_final: 0.8631 (m-70) REVERT: G 104 MET cc_start: 0.8432 (tpp) cc_final: 0.8061 (tpp) REVERT: G 150 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9126 (mt) REVERT: G 227 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7805 (p0) REVERT: I 485 MET cc_start: 0.8713 (mmm) cc_final: 0.8471 (mtt) REVERT: i 432 MET cc_start: 0.9224 (tpt) cc_final: 0.8764 (tpp) REVERT: i 586 MET cc_start: 0.8623 (mtp) cc_final: 0.8393 (mtm) REVERT: i 606 ASP cc_start: 0.8448 (t0) cc_final: 0.8033 (t0) REVERT: i 638 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: L 158 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5908 (t80) REVERT: M 69 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: m 139 MET cc_start: 0.8967 (tpp) cc_final: 0.8239 (tpp) REVERT: N 664 MET cc_start: 0.8807 (mmt) cc_final: 0.8361 (mmm) REVERT: N 672 MET cc_start: 0.8600 (mtp) cc_final: 0.8168 (mtp) REVERT: O 67 ASP cc_start: 0.8135 (t0) cc_final: 0.7869 (m-30) REVERT: O 84 ASP cc_start: 0.8643 (t0) cc_final: 0.8312 (t0) REVERT: O 85 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8091 (t0) REVERT: O 102 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8582 (tm-30) REVERT: O 104 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7516 (p0) REVERT: O 136 SER cc_start: 0.8752 (m) cc_final: 0.8292 (t) REVERT: P 122 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8156 (mp0) outliers start: 148 outliers final: 60 residues processed: 441 average time/residue: 1.2046 time to fit residues: 706.4649 Evaluate side-chains 400 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 322 time to evaluate : 5.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 217 GLU Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 448 MET Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1028 MET Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 646 MET Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain I residue 389 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 510 PHE Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 638 GLU Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain m residue 176 ASN Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 655 optimal weight: 0.9990 chunk 446 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 585 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 671 optimal weight: 9.9990 chunk 543 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 706 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 135 HIS ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 376 HIS ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN m 81 GLN O 120 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 61740 Z= 0.233 Angle : 0.519 12.103 83977 Z= 0.263 Chirality : 0.042 0.155 9475 Planarity : 0.004 0.054 11055 Dihedral : 3.838 51.672 8873 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 13.16 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 8157 helix: 1.52 (0.09), residues: 3308 sheet: -0.33 (0.16), residues: 1009 loop : -1.20 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.014 0.001 PHE B 867 TYR 0.019 0.001 TYR i 641 ARG 0.009 0.000 ARG F 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 333 time to evaluate : 5.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 81 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 307 MET cc_start: 0.9443 (mmm) cc_final: 0.9096 (mmt) REVERT: a 269 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9106 (tp) REVERT: a 289 MET cc_start: 0.9184 (mtp) cc_final: 0.8938 (mtt) REVERT: B 251 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5777 (m-80) REVERT: B 280 PHE cc_start: 0.8312 (m-10) cc_final: 0.7898 (t80) REVERT: B 306 MET cc_start: 0.8903 (mmm) cc_final: 0.8601 (mpp) REVERT: B 333 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6715 (pp20) REVERT: B 730 SER cc_start: 0.9143 (t) cc_final: 0.8885 (p) REVERT: C 111 MET cc_start: 0.8228 (mtp) cc_final: 0.7892 (mtp) REVERT: C 124 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6917 (p-90) REVERT: C 446 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8220 (tm-30) REVERT: c 153 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7353 (ppp) REVERT: c 255 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7774 (mtt) REVERT: c 988 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9151 (pp) REVERT: c 1028 MET cc_start: 0.8650 (ttm) cc_final: 0.7849 (tmm) REVERT: c 1163 MET cc_start: 0.8461 (mpp) cc_final: 0.8254 (mpp) REVERT: c 1270 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9176 (m) REVERT: D 78 MET cc_start: 0.8517 (mmm) cc_final: 0.8316 (mmm) REVERT: D 96 MET cc_start: 0.8006 (tpt) cc_final: 0.7777 (mmm) REVERT: D 125 MET cc_start: 0.9410 (ttp) cc_final: 0.8780 (tpt) REVERT: D 402 MET cc_start: 0.5524 (pmt) cc_final: 0.5268 (pmt) REVERT: D 510 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8620 (pp) REVERT: E 486 MET cc_start: 0.8258 (pmm) cc_final: 0.7952 (pmm) REVERT: E 513 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.4487 (mmt) REVERT: E 633 MET cc_start: 0.7386 (mpt) cc_final: 0.6832 (mpm) REVERT: E 646 MET cc_start: 0.4672 (ppp) cc_final: 0.3911 (ppp) REVERT: E 663 MET cc_start: 0.9015 (mtp) cc_final: 0.8652 (mmp) REVERT: E 713 MET cc_start: 0.4933 (mpt) cc_final: 0.2910 (tpp) REVERT: F 590 HIS cc_start: 0.8914 (m-70) cc_final: 0.8658 (m-70) REVERT: G 104 MET cc_start: 0.8403 (tpp) cc_final: 0.8039 (tpp) REVERT: G 150 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9113 (mt) REVERT: G 227 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7697 (p0) REVERT: I 485 MET cc_start: 0.8711 (mmm) cc_final: 0.8467 (mtt) REVERT: i 262 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7819 (pp) REVERT: i 383 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: i 432 MET cc_start: 0.9206 (tpt) cc_final: 0.8749 (tpp) REVERT: i 586 MET cc_start: 0.8627 (mtp) cc_final: 0.8414 (mtm) REVERT: i 606 ASP cc_start: 0.8454 (t0) cc_final: 0.8008 (t0) REVERT: i 638 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: K 283 ASP cc_start: 0.7735 (t0) cc_final: 0.7428 (t0) REVERT: L 158 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6075 (t80) REVERT: m 78 LYS cc_start: 0.9041 (tppt) cc_final: 0.8687 (tppt) REVERT: m 95 ASP cc_start: 0.8848 (t0) cc_final: 0.8629 (t0) REVERT: m 139 MET cc_start: 0.8966 (tpp) cc_final: 0.8249 (tpp) REVERT: N 664 MET cc_start: 0.8796 (mmt) cc_final: 0.8431 (mmm) REVERT: N 672 MET cc_start: 0.8594 (mtp) cc_final: 0.8181 (mtp) REVERT: O 67 ASP cc_start: 0.8130 (t0) cc_final: 0.7851 (m-30) REVERT: O 84 ASP cc_start: 0.8625 (t0) cc_final: 0.8287 (t0) REVERT: O 85 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (t0) REVERT: O 100 TYR cc_start: 0.8070 (t80) cc_final: 0.7381 (t80) REVERT: O 102 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8651 (tm-30) REVERT: O 136 SER cc_start: 0.8697 (m) cc_final: 0.8247 (t) REVERT: P 122 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8257 (mp0) outliers start: 127 outliers final: 55 residues processed: 432 average time/residue: 1.1848 time to fit residues: 686.3328 Evaluate side-chains 399 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 327 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 272 MET Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 624 ASP Chi-restraints excluded: chain i residue 638 GLU Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 188 ASN Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 121 ASN Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 264 optimal weight: 0.0370 chunk 708 optimal weight: 0.0060 chunk 155 optimal weight: 30.0000 chunk 461 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 787 optimal weight: 9.9990 chunk 653 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 260 optimal weight: 40.0000 chunk 413 optimal weight: 50.0000 overall best weight: 1.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN O 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 61740 Z= 0.184 Angle : 0.505 12.794 83977 Z= 0.254 Chirality : 0.041 0.149 9475 Planarity : 0.003 0.056 11055 Dihedral : 3.738 51.808 8871 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.31 % Allowed : 13.64 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 8157 helix: 1.65 (0.09), residues: 3315 sheet: -0.23 (0.16), residues: 1010 loop : -1.08 (0.10), residues: 3832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.018 0.001 PHE N 762 TYR 0.026 0.001 TYR m 133 ARG 0.008 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 338 time to evaluate : 5.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: A 81 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 307 MET cc_start: 0.9420 (mmm) cc_final: 0.9119 (mmt) REVERT: a 269 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9006 (tp) REVERT: a 289 MET cc_start: 0.9136 (mtp) cc_final: 0.8877 (mtt) REVERT: B 251 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: B 280 PHE cc_start: 0.8268 (m-10) cc_final: 0.7898 (t80) REVERT: B 306 MET cc_start: 0.8899 (mmm) cc_final: 0.8609 (mpp) REVERT: B 333 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6758 (pp20) REVERT: B 730 SER cc_start: 0.9117 (t) cc_final: 0.8860 (m) REVERT: B 988 MET cc_start: 0.8896 (mtm) cc_final: 0.8628 (mtp) REVERT: C 111 MET cc_start: 0.8213 (mtp) cc_final: 0.7897 (mtp) REVERT: C 124 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.7002 (p-90) REVERT: c 102 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: c 153 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7333 (ppp) REVERT: c 255 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (mtt) REVERT: c 313 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: c 447 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7794 (mt-10) REVERT: c 988 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9128 (pp) REVERT: c 1028 MET cc_start: 0.8624 (ttm) cc_final: 0.7836 (tmm) REVERT: c 1270 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9204 (m) REVERT: D 78 MET cc_start: 0.8532 (mmm) cc_final: 0.8301 (mmm) REVERT: D 125 MET cc_start: 0.9382 (ttp) cc_final: 0.8760 (tpt) REVERT: D 402 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.5247 (pmt) REVERT: D 510 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (pp) REVERT: E 486 MET cc_start: 0.8286 (pmm) cc_final: 0.7973 (pmm) REVERT: E 513 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.4473 (mmt) REVERT: E 633 MET cc_start: 0.7465 (mpt) cc_final: 0.6819 (mpm) REVERT: E 646 MET cc_start: 0.4383 (ppp) cc_final: 0.3702 (ppp) REVERT: E 663 MET cc_start: 0.8999 (mtp) cc_final: 0.8644 (mmp) REVERT: E 713 MET cc_start: 0.5086 (mpt) cc_final: 0.3057 (tpp) REVERT: F 211 MET cc_start: 0.8690 (mtm) cc_final: 0.8240 (mpp) REVERT: F 590 HIS cc_start: 0.8934 (m-70) cc_final: 0.8690 (m-70) REVERT: G 104 MET cc_start: 0.8387 (tpp) cc_final: 0.8015 (tpp) REVERT: G 150 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9090 (mt) REVERT: G 227 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7652 (p0) REVERT: I 485 MET cc_start: 0.8760 (mmm) cc_final: 0.8525 (mtt) REVERT: i 262 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7818 (pp) REVERT: i 383 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (mtp) REVERT: i 432 MET cc_start: 0.9203 (tpt) cc_final: 0.8661 (tpp) REVERT: i 586 MET cc_start: 0.8568 (mtp) cc_final: 0.8345 (mtm) REVERT: i 606 ASP cc_start: 0.8409 (t0) cc_final: 0.7965 (t0) REVERT: i 638 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: K 283 ASP cc_start: 0.7667 (t0) cc_final: 0.7357 (t0) REVERT: L 158 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6157 (t80) REVERT: M 69 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: m 78 LYS cc_start: 0.9037 (tppt) cc_final: 0.8714 (tppt) REVERT: m 139 MET cc_start: 0.8943 (tpp) cc_final: 0.8207 (tpp) REVERT: N 664 MET cc_start: 0.8766 (mmt) cc_final: 0.8330 (mmm) REVERT: N 672 MET cc_start: 0.8590 (mtp) cc_final: 0.8214 (mtp) REVERT: O 67 ASP cc_start: 0.8138 (t0) cc_final: 0.7861 (m-30) REVERT: O 99 GLN cc_start: 0.8863 (tt0) cc_final: 0.8604 (pp30) REVERT: O 102 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8636 (tm-30) REVERT: O 104 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7517 (p0) REVERT: O 136 SER cc_start: 0.8650 (m) cc_final: 0.8202 (t) REVERT: P 122 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8260 (mp0) outliers start: 128 outliers final: 60 residues processed: 438 average time/residue: 1.2143 time to fit residues: 709.7974 Evaluate side-chains 407 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 326 time to evaluate : 5.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 313 GLU Chi-restraints excluded: chain c residue 357 ASN Chi-restraints excluded: chain c residue 381 CYS Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1270 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain i residue 638 GLU Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 188 ASN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain N residue 588 PHE Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 634 MET Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 759 optimal weight: 50.0000 chunk 88 optimal weight: 8.9990 chunk 448 optimal weight: 0.0670 chunk 575 optimal weight: 4.9990 chunk 445 optimal weight: 10.0000 chunk 662 optimal weight: 4.9990 chunk 439 optimal weight: 20.0000 chunk 784 optimal weight: 50.0000 chunk 490 optimal weight: 5.9990 chunk 478 optimal weight: 5.9990 chunk 362 optimal weight: 0.3980 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 99 ASN B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN O 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 61740 Z= 0.330 Angle : 0.570 12.232 83977 Z= 0.287 Chirality : 0.043 0.192 9475 Planarity : 0.004 0.079 11055 Dihedral : 3.915 52.781 8871 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.36 % Allowed : 14.24 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 8157 helix: 1.63 (0.09), residues: 3326 sheet: -0.26 (0.16), residues: 1010 loop : -1.12 (0.10), residues: 3821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.018 0.001 PHE B 867 TYR 0.022 0.001 TYR N 607 ARG 0.006 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 327 time to evaluate : 5.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 307 MET cc_start: 0.9414 (mmm) cc_final: 0.9103 (mmt) REVERT: a 289 MET cc_start: 0.9154 (mtp) cc_final: 0.8892 (mtt) REVERT: a 307 MET cc_start: 0.9389 (mmm) cc_final: 0.9038 (mmm) REVERT: B 280 PHE cc_start: 0.8264 (m-10) cc_final: 0.7913 (t80) REVERT: B 306 MET cc_start: 0.8904 (mmm) cc_final: 0.8611 (mpp) REVERT: B 730 SER cc_start: 0.9129 (t) cc_final: 0.8880 (m) REVERT: C 124 TRP cc_start: 0.7249 (OUTLIER) cc_final: 0.6935 (p-90) REVERT: c 153 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7373 (ppp) REVERT: c 255 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: c 988 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9163 (pp) REVERT: c 1257 MET cc_start: 0.9187 (mtm) cc_final: 0.8968 (mtm) REVERT: D 78 MET cc_start: 0.8545 (mmm) cc_final: 0.8313 (mmm) REVERT: D 125 MET cc_start: 0.9403 (ttp) cc_final: 0.8770 (tpt) REVERT: D 402 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.5230 (pmt) REVERT: D 510 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8642 (pp) REVERT: D 871 ASP cc_start: 0.9384 (m-30) cc_final: 0.9116 (p0) REVERT: E 486 MET cc_start: 0.8293 (pmm) cc_final: 0.7912 (pmm) REVERT: E 513 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.4410 (mmt) REVERT: E 633 MET cc_start: 0.7475 (mpt) cc_final: 0.6889 (mpm) REVERT: E 646 MET cc_start: 0.4916 (ppp) cc_final: 0.4433 (ppp) REVERT: E 663 MET cc_start: 0.9022 (mtp) cc_final: 0.8637 (mpp) REVERT: E 713 MET cc_start: 0.5048 (mpt) cc_final: 0.2966 (tpp) REVERT: F 211 MET cc_start: 0.8723 (mtm) cc_final: 0.8424 (mpp) REVERT: F 590 HIS cc_start: 0.8956 (m-70) cc_final: 0.8721 (m-70) REVERT: G 104 MET cc_start: 0.8399 (tpp) cc_final: 0.8023 (tpp) REVERT: G 150 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9124 (mt) REVERT: G 227 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7645 (p0) REVERT: i 262 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7837 (pp) REVERT: i 383 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: i 432 MET cc_start: 0.9193 (tpt) cc_final: 0.8643 (tpp) REVERT: i 586 MET cc_start: 0.8575 (mtp) cc_final: 0.8355 (mtm) REVERT: i 606 ASP cc_start: 0.8447 (t0) cc_final: 0.7996 (t0) REVERT: L 158 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6012 (t80) REVERT: M 69 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8838 (m-30) REVERT: M 172 ASP cc_start: 0.8500 (m-30) cc_final: 0.8248 (m-30) REVERT: m 78 LYS cc_start: 0.9108 (tppt) cc_final: 0.8786 (tppt) REVERT: m 139 MET cc_start: 0.8968 (tpp) cc_final: 0.8216 (tpp) REVERT: N 614 ARG cc_start: 0.7632 (pmm-80) cc_final: 0.7113 (pmm-80) REVERT: N 672 MET cc_start: 0.8631 (mtp) cc_final: 0.8245 (mtp) REVERT: O 67 ASP cc_start: 0.8173 (t0) cc_final: 0.7895 (m-30) REVERT: O 99 GLN cc_start: 0.8809 (tt0) cc_final: 0.8338 (tm-30) REVERT: O 102 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8565 (tm-30) REVERT: O 104 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7634 (p0) REVERT: O 136 SER cc_start: 0.8596 (m) cc_final: 0.8151 (t) REVERT: P 122 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8291 (mp0) outliers start: 131 outliers final: 74 residues processed: 425 average time/residue: 1.2422 time to fit residues: 711.0152 Evaluate side-chains 406 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 317 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 357 ASN Chi-restraints excluded: chain c residue 381 CYS Chi-restraints excluded: chain c residue 448 MET Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1234 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 513 MET Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 529 MET Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain I residue 389 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 510 PHE Chi-restraints excluded: chain i residue 539 HIS Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 188 ASN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain N residue 588 PHE Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 485 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 468 optimal weight: 0.4980 chunk 236 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 498 optimal weight: 50.0000 chunk 534 optimal weight: 6.9990 chunk 387 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 616 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN O 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61740 Z= 0.227 Angle : 0.536 13.346 83977 Z= 0.268 Chirality : 0.042 0.199 9475 Planarity : 0.004 0.067 11055 Dihedral : 3.856 52.340 8871 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.02 % Allowed : 14.96 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.10), residues: 8157 helix: 1.70 (0.09), residues: 3324 sheet: -0.18 (0.16), residues: 1006 loop : -1.04 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.016 0.001 PHE J 162 TYR 0.026 0.001 TYR N 607 ARG 0.007 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 326 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 289 MET cc_start: 0.8628 (ptt) cc_final: 0.8248 (pmm) REVERT: a 289 MET cc_start: 0.9111 (mtp) cc_final: 0.8849 (mtt) REVERT: a 307 MET cc_start: 0.9399 (mmm) cc_final: 0.9044 (mmm) REVERT: B 280 PHE cc_start: 0.8251 (m-10) cc_final: 0.7915 (t80) REVERT: B 306 MET cc_start: 0.8902 (mmm) cc_final: 0.8614 (mpp) REVERT: B 333 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6772 (pp20) REVERT: B 730 SER cc_start: 0.9050 (t) cc_final: 0.8827 (m) REVERT: B 988 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8647 (mtp) REVERT: C 111 MET cc_start: 0.7698 (mtp) cc_final: 0.7423 (mtp) REVERT: c 153 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7370 (ppp) REVERT: c 255 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7733 (mtt) REVERT: c 447 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7805 (mt-10) REVERT: c 988 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9155 (pp) REVERT: c 1028 MET cc_start: 0.8617 (ttm) cc_final: 0.7855 (tmm) REVERT: D 78 MET cc_start: 0.8607 (mmm) cc_final: 0.8352 (mmm) REVERT: D 125 MET cc_start: 0.9407 (ttp) cc_final: 0.8784 (tpt) REVERT: D 510 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (pp) REVERT: D 871 ASP cc_start: 0.9404 (m-30) cc_final: 0.9141 (p0) REVERT: E 486 MET cc_start: 0.8389 (pmm) cc_final: 0.8023 (pmm) REVERT: E 633 MET cc_start: 0.7590 (mpt) cc_final: 0.7056 (mpm) REVERT: E 646 MET cc_start: 0.4870 (ppp) cc_final: 0.4485 (ppp) REVERT: E 663 MET cc_start: 0.9037 (mtp) cc_final: 0.8603 (mpp) REVERT: E 713 MET cc_start: 0.5036 (mpt) cc_final: 0.2993 (tpp) REVERT: F 211 MET cc_start: 0.8733 (mtm) cc_final: 0.8445 (mpp) REVERT: F 590 HIS cc_start: 0.8964 (m-70) cc_final: 0.8723 (m-70) REVERT: G 104 MET cc_start: 0.8391 (tpp) cc_final: 0.8013 (tpp) REVERT: G 150 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9099 (mt) REVERT: G 227 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7613 (p0) REVERT: i 262 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7840 (pp) REVERT: i 383 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8354 (mtm) REVERT: i 432 MET cc_start: 0.9187 (tpt) cc_final: 0.8639 (tpp) REVERT: i 586 MET cc_start: 0.8544 (mtp) cc_final: 0.8342 (mtm) REVERT: i 606 ASP cc_start: 0.8437 (t0) cc_final: 0.7970 (t0) REVERT: J 240 MET cc_start: 0.8243 (mmm) cc_final: 0.7877 (mmm) REVERT: L 158 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6124 (t80) REVERT: M 69 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8786 (m-30) REVERT: m 78 LYS cc_start: 0.9119 (tppt) cc_final: 0.8751 (tppt) REVERT: m 139 MET cc_start: 0.8949 (tpp) cc_final: 0.8181 (tpp) REVERT: m 169 MET cc_start: 0.8460 (ttm) cc_final: 0.8239 (ttm) REVERT: N 664 MET cc_start: 0.8585 (mmt) cc_final: 0.8152 (mmm) REVERT: N 672 MET cc_start: 0.8629 (mtp) cc_final: 0.8250 (mtp) REVERT: O 67 ASP cc_start: 0.8158 (t0) cc_final: 0.7865 (m-30) REVERT: O 99 GLN cc_start: 0.8814 (tt0) cc_final: 0.8355 (tm-30) REVERT: O 102 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8565 (tm-30) REVERT: O 104 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7537 (p0) REVERT: O 136 SER cc_start: 0.8575 (m) cc_final: 0.8130 (t) REVERT: P 122 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8332 (mp0) outliers start: 112 outliers final: 71 residues processed: 414 average time/residue: 1.2609 time to fit residues: 697.3983 Evaluate side-chains 400 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 316 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 227 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 357 ASN Chi-restraints excluded: chain c residue 381 CYS Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 510 ILE Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain E residue 757 ILE Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 529 MET Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 510 PHE Chi-restraints excluded: chain i residue 539 HIS Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 188 ASN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 89 ASN Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain N residue 588 PHE Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 713 optimal weight: 0.0060 chunk 751 optimal weight: 20.0000 chunk 685 optimal weight: 4.9990 chunk 731 optimal weight: 1.9990 chunk 440 optimal weight: 40.0000 chunk 318 optimal weight: 2.9990 chunk 574 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 660 optimal weight: 4.9990 chunk 691 optimal weight: 4.9990 chunk 728 optimal weight: 3.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 61740 Z= 0.290 Angle : 0.571 14.770 83977 Z= 0.284 Chirality : 0.043 0.239 9475 Planarity : 0.004 0.083 11055 Dihedral : 3.922 52.837 8871 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.11 % Allowed : 15.14 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.10), residues: 8157 helix: 1.68 (0.09), residues: 3327 sheet: -0.19 (0.16), residues: 1007 loop : -1.04 (0.10), residues: 3823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.016 0.001 PHE B 867 TYR 0.027 0.001 TYR N 607 ARG 0.014 0.000 ARG F 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 325 time to evaluate : 5.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 307 MET cc_start: 0.9385 (mmm) cc_final: 0.9121 (mmt) REVERT: a 289 MET cc_start: 0.9139 (mtp) cc_final: 0.8888 (mtt) REVERT: a 307 MET cc_start: 0.9440 (mmm) cc_final: 0.9079 (mmm) REVERT: B 280 PHE cc_start: 0.8302 (m-10) cc_final: 0.7986 (t80) REVERT: B 306 MET cc_start: 0.8928 (mmm) cc_final: 0.8644 (mpp) REVERT: B 333 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6778 (pp20) REVERT: B 730 SER cc_start: 0.9038 (t) cc_final: 0.8815 (m) REVERT: B 988 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: C 111 MET cc_start: 0.7700 (mtp) cc_final: 0.7420 (mtp) REVERT: c 153 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7388 (ppp) REVERT: c 255 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: c 988 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9151 (pp) REVERT: c 1028 MET cc_start: 0.8619 (ttm) cc_final: 0.7772 (tmm) REVERT: c 1322 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8893 (pp) REVERT: D 78 MET cc_start: 0.8609 (mmm) cc_final: 0.8351 (mmm) REVERT: D 125 MET cc_start: 0.9389 (ttp) cc_final: 0.8844 (tpt) REVERT: D 871 ASP cc_start: 0.9393 (m-30) cc_final: 0.9136 (p0) REVERT: E 486 MET cc_start: 0.8406 (pmm) cc_final: 0.8031 (pmm) REVERT: E 513 MET cc_start: 0.4430 (mmt) cc_final: 0.4201 (mmt) REVERT: E 633 MET cc_start: 0.7595 (mpt) cc_final: 0.7048 (mpm) REVERT: E 646 MET cc_start: 0.4890 (ppp) cc_final: 0.4516 (ppp) REVERT: E 663 MET cc_start: 0.9050 (mtp) cc_final: 0.8606 (mpp) REVERT: E 713 MET cc_start: 0.5107 (mpt) cc_final: 0.3208 (tpp) REVERT: F 211 MET cc_start: 0.8734 (mtm) cc_final: 0.8443 (mpp) REVERT: F 590 HIS cc_start: 0.8977 (m-70) cc_final: 0.8721 (m-70) REVERT: G 104 MET cc_start: 0.8383 (tpp) cc_final: 0.8014 (tpp) REVERT: G 150 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9095 (mt) REVERT: G 227 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7685 (p0) REVERT: i 262 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7822 (pp) REVERT: i 383 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (mtm) REVERT: i 432 MET cc_start: 0.9193 (tpt) cc_final: 0.8635 (tpp) REVERT: i 586 MET cc_start: 0.8580 (mtp) cc_final: 0.8378 (mtm) REVERT: i 606 ASP cc_start: 0.8450 (t0) cc_final: 0.7995 (t0) REVERT: L 158 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6177 (t80) REVERT: M 69 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8870 (m-30) REVERT: M 172 ASP cc_start: 0.8484 (m-30) cc_final: 0.8230 (m-30) REVERT: m 78 LYS cc_start: 0.9253 (tppt) cc_final: 0.8890 (tppt) REVERT: m 139 MET cc_start: 0.8972 (tpp) cc_final: 0.8234 (tpp) REVERT: N 614 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7002 (mpp-170) REVERT: N 664 MET cc_start: 0.8594 (mmt) cc_final: 0.8180 (mmm) REVERT: N 672 MET cc_start: 0.8625 (mtp) cc_final: 0.8235 (mtp) REVERT: O 67 ASP cc_start: 0.8175 (t0) cc_final: 0.7877 (m-30) REVERT: O 99 GLN cc_start: 0.8822 (tt0) cc_final: 0.8356 (tm-30) REVERT: O 102 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8554 (tm-30) REVERT: O 104 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7317 (p0) REVERT: O 136 SER cc_start: 0.8572 (m) cc_final: 0.8122 (t) REVERT: P 62 MET cc_start: 0.9325 (mmm) cc_final: 0.9059 (mmm) REVERT: P 122 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8343 (mp0) REVERT: P 133 GLU cc_start: 0.8673 (pt0) cc_final: 0.8083 (mp0) outliers start: 117 outliers final: 76 residues processed: 418 average time/residue: 1.2278 time to fit residues: 689.0483 Evaluate side-chains 410 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 320 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 357 ASN Chi-restraints excluded: chain c residue 381 CYS Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1322 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 529 MET Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 510 PHE Chi-restraints excluded: chain i residue 539 HIS Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 188 ASN Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain m residue 138 ASP Chi-restraints excluded: chain N residue 588 PHE Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 614 ARG Chi-restraints excluded: chain N residue 693 LEU Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 480 optimal weight: 2.9990 chunk 773 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 366 optimal weight: 5.9990 chunk 537 optimal weight: 3.9990 chunk 810 optimal weight: 9.9990 chunk 746 optimal weight: 50.0000 chunk 645 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 498 optimal weight: 40.0000 chunk 395 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 HIS ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 61740 Z= 0.288 Angle : 0.573 15.183 83977 Z= 0.286 Chirality : 0.043 0.205 9475 Planarity : 0.004 0.106 11055 Dihedral : 3.947 52.820 8871 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.80 % Allowed : 15.48 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 8157 helix: 1.68 (0.09), residues: 3319 sheet: -0.20 (0.16), residues: 1020 loop : -1.03 (0.10), residues: 3818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.017 0.001 PHE J 162 TYR 0.027 0.001 TYR N 607 ARG 0.011 0.000 ARG F 537 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16314 Ramachandran restraints generated. 8157 Oldfield, 0 Emsley, 8157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 323 time to evaluate : 5.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: A 307 MET cc_start: 0.9400 (mmm) cc_final: 0.9122 (mmt) REVERT: a 289 MET cc_start: 0.9129 (mtp) cc_final: 0.8878 (mtt) REVERT: B 280 PHE cc_start: 0.8311 (m-10) cc_final: 0.8096 (t80) REVERT: B 306 MET cc_start: 0.8933 (mmm) cc_final: 0.8649 (mpp) REVERT: B 333 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6780 (pp20) REVERT: B 730 SER cc_start: 0.9045 (t) cc_final: 0.8824 (m) REVERT: B 988 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8588 (mtp) REVERT: C 111 MET cc_start: 0.7812 (mtp) cc_final: 0.7544 (mtp) REVERT: c 153 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7399 (ppp) REVERT: c 255 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7812 (mtt) REVERT: c 447 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7795 (mt-10) REVERT: c 951 MET cc_start: 0.8090 (mpm) cc_final: 0.7836 (mmm) REVERT: c 988 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9150 (pp) REVERT: c 1028 MET cc_start: 0.8622 (ttm) cc_final: 0.7764 (tmm) REVERT: c 1322 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8887 (pp) REVERT: D 78 MET cc_start: 0.8613 (mmm) cc_final: 0.8352 (mmm) REVERT: D 125 MET cc_start: 0.9385 (ttp) cc_final: 0.8844 (tpt) REVERT: D 871 ASP cc_start: 0.9401 (m-30) cc_final: 0.9147 (p0) REVERT: E 486 MET cc_start: 0.8391 (pmm) cc_final: 0.7999 (pmm) REVERT: E 633 MET cc_start: 0.7602 (mpt) cc_final: 0.7056 (mpm) REVERT: E 646 MET cc_start: 0.4792 (ppp) cc_final: 0.4368 (ppp) REVERT: E 663 MET cc_start: 0.9034 (mtp) cc_final: 0.8608 (mpp) REVERT: E 713 MET cc_start: 0.5131 (mpt) cc_final: 0.4882 (mpt) REVERT: F 124 MET cc_start: 0.9404 (mmt) cc_final: 0.9127 (mmm) REVERT: F 211 MET cc_start: 0.8723 (mtm) cc_final: 0.8449 (mpp) REVERT: F 590 HIS cc_start: 0.8962 (m-70) cc_final: 0.8697 (m-70) REVERT: G 104 MET cc_start: 0.8380 (tpp) cc_final: 0.8033 (tpp) REVERT: G 150 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9133 (mt) REVERT: G 227 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (p0) REVERT: i 262 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7834 (pp) REVERT: i 383 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: i 432 MET cc_start: 0.9193 (tpt) cc_final: 0.8634 (tpp) REVERT: i 586 MET cc_start: 0.8604 (mtp) cc_final: 0.8395 (mtm) REVERT: i 606 ASP cc_start: 0.8456 (t0) cc_final: 0.8005 (t0) REVERT: L 158 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6192 (t80) REVERT: M 69 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8857 (m-30) REVERT: m 78 LYS cc_start: 0.9237 (tppt) cc_final: 0.8881 (tppt) REVERT: m 139 MET cc_start: 0.8956 (tpp) cc_final: 0.8217 (tpp) REVERT: m 170 MET cc_start: 0.9058 (mpp) cc_final: 0.8822 (pmm) REVERT: N 614 ARG cc_start: 0.7812 (pmt100) cc_final: 0.7415 (pmt170) REVERT: N 664 MET cc_start: 0.8613 (mmt) cc_final: 0.8168 (mmm) REVERT: N 672 MET cc_start: 0.8624 (mtp) cc_final: 0.8233 (mtp) REVERT: O 67 ASP cc_start: 0.8160 (t0) cc_final: 0.7836 (m-30) REVERT: O 96 GLU cc_start: 0.8399 (tt0) cc_final: 0.8162 (tm-30) REVERT: O 99 GLN cc_start: 0.8804 (tt0) cc_final: 0.8318 (tm-30) REVERT: O 102 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8551 (tm-30) REVERT: O 104 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7236 (p0) REVERT: O 136 SER cc_start: 0.8567 (m) cc_final: 0.8115 (t) REVERT: P 122 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8375 (mp0) outliers start: 100 outliers final: 75 residues processed: 400 average time/residue: 1.2309 time to fit residues: 658.9187 Evaluate side-chains 408 residues out of total 7234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 320 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain a residue 43 ASP Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 TRP Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 147 VAL Chi-restraints excluded: chain c residue 153 MET Chi-restraints excluded: chain c residue 245 ILE Chi-restraints excluded: chain c residue 255 MET Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 357 ASN Chi-restraints excluded: chain c residue 381 CYS Chi-restraints excluded: chain c residue 988 ILE Chi-restraints excluded: chain c residue 1042 ASN Chi-restraints excluded: chain c residue 1128 THR Chi-restraints excluded: chain c residue 1232 VAL Chi-restraints excluded: chain c residue 1265 ILE Chi-restraints excluded: chain c residue 1322 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 740 VAL Chi-restraints excluded: chain D residue 742 MET Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 521 ASN Chi-restraints excluded: chain E residue 685 VAL Chi-restraints excluded: chain E residue 708 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 529 MET Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 411 ASP Chi-restraints excluded: chain i residue 262 LEU Chi-restraints excluded: chain i residue 383 MET Chi-restraints excluded: chain i residue 418 LYS Chi-restraints excluded: chain i residue 510 PHE Chi-restraints excluded: chain i residue 539 HIS Chi-restraints excluded: chain i residue 558 THR Chi-restraints excluded: chain J residue 116 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 412 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 158 PHE Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain m residue 101 CYS Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 130 ASP Chi-restraints excluded: chain m residue 131 ASP Chi-restraints excluded: chain m residue 138 ASP Chi-restraints excluded: chain N residue 588 PHE Chi-restraints excluded: chain N residue 609 ARG Chi-restraints excluded: chain N residue 693 LEU Chi-restraints excluded: chain N residue 701 VAL Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 814 random chunks: chunk 512 optimal weight: 30.0000 chunk 687 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 595 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 646 optimal weight: 0.6980 chunk 270 optimal weight: 50.0000 chunk 664 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 687 ASN ** E 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 243 GLN ** K 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 ASN O 61 GLN O 120 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.084836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057019 restraints weight = 246446.312| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.42 r_work: 0.2897 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 61740 Z= 0.255 Angle : 0.568 14.872 83977 Z= 0.283 Chirality : 0.043 0.291 9475 Planarity : 0.004 0.107 11055 Dihedral : 3.932 53.878 8871 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.96 % Allowed : 15.39 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.10), residues: 8157 helix: 1.68 (0.09), residues: 3326 sheet: -0.22 (0.16), residues: 1030 loop : -1.00 (0.10), residues: 3801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 486 HIS 0.008 0.001 HIS D 828 PHE 0.015 0.001 PHE J 162 TYR 0.029 0.001 TYR N 607 ARG 0.010 0.000 ARG F 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15330.66 seconds wall clock time: 266 minutes 46.35 seconds (16006.35 seconds total)