Starting phenix.real_space_refine (version: dev) on Thu Dec 15 16:29:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euy_24420/12_2022/8euy_24420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euy_24420/12_2022/8euy_24420.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/8euy_24420/12_2022/8euy_24420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euy_24420/12_2022/8euy_24420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euy_24420/12_2022/8euy_24420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euy_24420/12_2022/8euy_24420.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "4 GLU 37": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "S TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 40": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "h GLU 14": "OE1" <-> "OE2" Residue "h GLU 18": "OE1" <-> "OE2" Residue "h GLU 26": "OE1" <-> "OE2" Residue "i GLU 44": "OE1" <-> "OE2" Residue "i GLU 86": "OE1" <-> "OE2" Residue "m GLU 212": "OE1" <-> "OE2" Residue "v GLU 142": "OE1" <-> "OE2" Residue "x GLU 35": "OE1" <-> "OE2" Residue "x TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 80249 Number of models: 1 Model: "" Number of chains: 41 Chain: "1" Number of atoms: 30681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1433, 30681 Classifications: {'RNA': 1433} Modifications used: {'rna2p_pur': 148, 'rna2p_pyr': 96, 'rna3p_pur': 658, 'rna3p_pyr': 531} Link IDs: {'rna2p': 244, 'rna3p': 1188} Chain breaks: 24 Chain: "2" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2762 Classifications: {'RNA': 130} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 8, 'rna3p_pur': 51, 'rna3p_pyr': 56} Link IDs: {'rna2p': 23, 'rna3p': 106} Chain breaks: 3 Chain: "3" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1596 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "4" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1770 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "5" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2686 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "6" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1160 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 17, 'rna3p_pur': 14, 'rna3p_pyr': 21} Link IDs: {'rna2p': 21, 'rna3p': 34} Chain breaks: 2 Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2057 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2641 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2572 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3001 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 16, 'TRANS': 389} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 128 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1328 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain: "F" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1944 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 228} Chain: "G" Number of atoms: 1273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 164, 1265 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 164, 1265 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 bond proxies already assigned to first conformer: 1274 Chain: "H" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 764 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 267 Chain: "J" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 444 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "K" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1205 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 228} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 943 Unresolved non-hydrogen dihedrals: 621 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1487 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "P" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1139 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "Q" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1047 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 129} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1402 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 554 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 137 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 594 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 229 Chain: "e" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 768 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "m" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 725 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "o" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 992 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "r" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 249 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 121 Chain: "t" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 216 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 506 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 211 Chain: "v" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 1 Chain: "x" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2516 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 293} Chain: "y" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 974 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 722 Unresolved non-hydrogen dihedrals: 431 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 305 Chain: "T" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 147 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 72107 SG CYS j 19 91.588 92.995 166.559 1.00 22.92 S ATOM 72135 SG CYS j 22 93.923 93.747 163.568 1.00 30.90 S ATOM 72231 SG CYS j 34 92.555 90.304 163.957 1.00 19.00 S ATOM 72248 SG CYS j 37 95.048 91.633 166.519 1.00 29.92 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP G 227 " occ=0.04 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.96 Time building chain proxies: 34.37, per 1000 atoms: 0.43 Number of scatterers: 80249 At special positions: 0 Unit cell: (230.02, 196.1, 312.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 1619 15.00 O 19459 8.00 N 14804 7.00 C 44250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.91 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " Number of angles added : 6 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11586 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 61 sheets defined 42.8% alpha, 15.8% beta 496 base pairs and 938 stacking pairs defined. Time for finding SS restraints: 25.73 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 67 through 70 Processing helix chain '3' and resid 72 through 75 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 128 Processing helix chain '3' and resid 137 through 156 removed outlier: 3.716A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 171 Processing helix chain '3' and resid 182 through 194 Processing helix chain '4' and resid 9 through 13 Processing helix chain '4' and resid 15 through 31 removed outlier: 3.850A pdb=" N GLN 4 27 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 54 Processing helix chain '4' and resid 57 through 71 removed outlier: 3.622A pdb=" N SER 4 65 " --> pdb=" O GLN 4 61 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP 4 66 " --> pdb=" O GLN 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 93 removed outlier: 3.573A pdb=" N PHE 4 83 " --> pdb=" O ASN 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 126 removed outlier: 4.298A pdb=" N ASP 4 104 " --> pdb=" O ILE 4 100 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS 4 105 " --> pdb=" O LEU 4 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE 4 106 " --> pdb=" O ARG 4 102 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 4 126 " --> pdb=" O GLN 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 144 Processing helix chain '4' and resid 154 through 173 removed outlier: 3.963A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR 4 166 " --> pdb=" O ALA 4 162 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU 4 167 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 193 Processing helix chain '4' and resid 195 through 206 Proline residue: 4 203 - end of helix Processing helix chain '4' and resid 209 through 213 removed outlier: 3.662A pdb=" N TYR 4 212 " --> pdb=" O VAL 4 209 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 43 Processing helix chain '5' and resid 83 through 87 Processing helix chain '5' and resid 205 through 208 removed outlier: 3.762A pdb=" N ILE 5 208 " --> pdb=" O GLU 5 205 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 205 through 208' Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 84 through 94 removed outlier: 4.015A pdb=" N GLU A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 250 through 283 removed outlier: 3.717A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.831A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.887A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 removed outlier: 4.071A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 4.051A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.583A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.606A pdb=" N LEU C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.545A pdb=" N SER C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 99 through 108 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.608A pdb=" N ALA D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 155 removed outlier: 3.740A pdb=" N LEU D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Proline residue: D 146 - end of helix Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 200 through 211 removed outlier: 3.741A pdb=" N ASP D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.548A pdb=" N GLY D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.867A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 removed outlier: 4.347A pdb=" N GLU D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.538A pdb=" N HIS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 445 Processing helix chain 'D' and resid 446 through 455 removed outlier: 3.954A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 483 through 503 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.189A pdb=" N GLU E 142 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.656A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.939A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 180 Processing helix chain 'F' and resid 16 through 80 removed outlier: 3.624A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.883A pdb=" N MET F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.918A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 198 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.380A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.589A pdb=" N ILE G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.516A pdb=" N ARG G 231 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.536A pdb=" N ARG H 24 " --> pdb=" O ILE H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 85 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 160 removed outlier: 3.580A pdb=" N GLN J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 94 through 106 removed outlier: 4.331A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 109 No H-bonds generated for 'chain 'K' and resid 107 through 109' Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.679A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 136 Processing helix chain 'K' and resid 154 through 160 removed outlier: 3.854A pdb=" N PHE K 158 " --> pdb=" O LEU K 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN K 160 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.398A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.518A pdb=" N LEU L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 162 Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 61 removed outlier: 3.673A pdb=" N ASN O 51 " --> pdb=" O HIS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 removed outlier: 3.709A pdb=" N MET O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.126A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 145 removed outlier: 3.876A pdb=" N GLU O 145 " --> pdb=" O ARG O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 186 removed outlier: 4.845A pdb=" N GLU O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG O 160 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS O 178 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE O 179 " --> pdb=" O LYS O 175 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 removed outlier: 3.586A pdb=" N LEU O 192 " --> pdb=" O VAL O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 196 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.019A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'S' and resid 32 through 48 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.965A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 41 through 64 Processing helix chain 'b' and resid 104 through 119 removed outlier: 3.822A pdb=" N TYR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 143 Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 442 through 445 removed outlier: 4.035A pdb=" N VAL b 445 " --> pdb=" O ALA b 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 442 through 445' Processing helix chain 'e' and resid 37 through 42 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.519A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU e 81 " --> pdb=" O SER e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 84 No H-bonds generated for 'chain 'e' and resid 82 through 84' Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 40 through 44 Processing helix chain 'f' and resid 59 through 63 Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.550A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.597A pdb=" N ALA h 17 " --> pdb=" O GLN h 13 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU h 18 " --> pdb=" O GLU h 14 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA h 36 " --> pdb=" O VAL h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 72 Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 46 Processing helix chain 'i' and resid 49 through 61 removed outlier: 3.507A pdb=" N ASN i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 99 removed outlier: 3.562A pdb=" N ALA i 98 " --> pdb=" O SER i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.711A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 75 removed outlier: 3.563A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'm' and resid 221 through 226 removed outlier: 3.577A pdb=" N ARG m 224 " --> pdb=" O PRO m 221 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA m 226 " --> pdb=" O ARG m 223 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 256 Processing helix chain 'o' and resid 117 through 129 removed outlier: 3.915A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 Processing helix chain 'o' and resid 188 through 192 Processing helix chain 'o' and resid 202 through 211 Processing helix chain 'o' and resid 221 through 238 Processing helix chain 'r' and resid 5 through 13 Processing helix chain 'r' and resid 18 through 42 removed outlier: 4.176A pdb=" N GLU r 22 " --> pdb=" O PHE r 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 54 Processing helix chain 't' and resid 53 through 73 removed outlier: 3.917A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.592A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.612A pdb=" N ASN u 92 " --> pdb=" O ALA u 88 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 12 Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 53 Processing helix chain 'v' and resid 120 through 125 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.529A pdb=" N LEU v 170 " --> pdb=" O TYR v 166 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS v 173 " --> pdb=" O ARG v 169 " (cutoff:3.500A) Processing helix chain 'v' and resid 179 through 185 Processing helix chain 'v' and resid 194 through 207 Processing helix chain 'x' and resid 6 through 39 Processing helix chain 'x' and resid 39 through 50 removed outlier: 3.920A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 79 Processing helix chain 'x' and resid 83 through 88 removed outlier: 3.542A pdb=" N PHE x 87 " --> pdb=" O PHE x 83 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 119 removed outlier: 3.690A pdb=" N GLU x 114 " --> pdb=" O ASP x 110 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 141 Processing helix chain 'x' and resid 181 through 185 Processing helix chain 'x' and resid 205 through 217 Processing helix chain 'x' and resid 224 through 227 Processing helix chain 'x' and resid 296 through 300 Processing helix chain 'y' and resid 12 through 16 Processing helix chain 'y' and resid 31 through 42 Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.698A pdb=" N LEU y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 186 through 190 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 56 Processing sheet with id=AA3, first strand: chain '3' and resid 132 through 135 Processing sheet with id=AA4, first strand: chain '5' and resid 33 through 37 removed outlier: 4.602A pdb=" N GLN 5 11 " --> pdb=" O ASP 5 7 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS 5 2 " --> pdb=" O ILE 5 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 5 338 " --> pdb=" O GLY 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 45 through 47 removed outlier: 6.565A pdb=" N ALA 5 58 " --> pdb=" O LEU 5 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 45 through 47 removed outlier: 6.565A pdb=" N ALA 5 58 " --> pdb=" O LEU 5 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 5 78 " --> pdb=" O CYS 5 66 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN 5 68 " --> pdb=" O LEU 5 76 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU 5 76 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 96 through 98 Processing sheet with id=AA8, first strand: chain '5' and resid 111 through 114 Processing sheet with id=AA9, first strand: chain '5' and resid 132 through 135 removed outlier: 5.318A pdb=" N GLY 5 147 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP 5 151 " --> pdb=" O GLY 5 147 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 5 180 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER 5 156 " --> pdb=" O LYS 5 178 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS 5 178 " --> pdb=" O SER 5 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 198 through 203 removed outlier: 6.381A pdb=" N ILE 5 228 " --> pdb=" O THR 5 199 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE 5 201 " --> pdb=" O ALA 5 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA 5 226 " --> pdb=" O ILE 5 201 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE 5 203 " --> pdb=" O HIS 5 224 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N HIS 5 224 " --> pdb=" O PHE 5 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 256 through 262 removed outlier: 3.741A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE 5 277 " --> pdb=" O ARG 5 290 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG 5 290 " --> pdb=" O ILE 5 277 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE 5 279 " --> pdb=" O ILE 5 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 298 through 304 removed outlier: 3.505A pdb=" N SER 5 300 " --> pdb=" O THR 5 311 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY 5 312 " --> pdb=" O ASN 5 316 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP 5 321 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.918A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 74 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 47 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS A 76 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER A 49 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 50 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU A 234 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N VAL A 241 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.918A pdb=" N VAL A 45 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 74 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 47 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS A 76 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER A 49 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 48 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 50 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 129 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE A 225 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 221 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLU A 204 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 202 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 225 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU A 149 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.076A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.076A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 282 through 284 removed outlier: 6.068A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.120A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 218 through 220 Processing sheet with id=AC2, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.773A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC4, first strand: chain 'D' and resid 129 through 131 removed outlier: 6.493A pdb=" N ILE D 165 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.800A pdb=" N VAL D 339 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N CYS D 392 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 341 " --> pdb=" O CYS D 392 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE D 408 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE D 440 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN D 410 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D 315 " --> pdb=" O PHE D 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.915A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 82 through 84 Processing sheet with id=AC8, first strand: chain 'F' and resid 212 through 213 removed outlier: 4.135A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AD1, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 11 Processing sheet with id=AD3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.642A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 87 through 92 removed outlier: 5.466A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 198 through 205 removed outlier: 5.989A pdb=" N SER K 198 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR K 59 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N MET K 200 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU K 57 " --> pdb=" O MET K 200 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS K 202 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU K 55 " --> pdb=" O LYS K 202 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY K 204 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU K 241 " --> pdb=" O PRO K 250 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 72 through 75 Processing sheet with id=AD7, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.576A pdb=" N ALA K 87 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG K 113 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.343A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AE1, first strand: chain 'L' and resid 123 through 126 removed outlier: 4.797A pdb=" N LYS h 117 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.560A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.573A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 7 through 11 removed outlier: 5.964A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE6, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.655A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.143A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.693A pdb=" N THR Q 81 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 55 through 62 removed outlier: 6.555A pdb=" N VAL S 9 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE S 60 " --> pdb=" O GLN S 7 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN S 7 " --> pdb=" O ILE S 60 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU S 62 " --> pdb=" O GLU S 5 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU S 5 " --> pdb=" O GLU S 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 87 through 95 removed outlier: 6.524A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 35 through 40 removed outlier: 6.260A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 78 through 82 removed outlier: 6.547A pdb=" N ALA V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 87 through 88 removed outlier: 3.624A pdb=" N MET u 20 " --> pdb=" O TYR V 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF6, first strand: chain 'Y' and resid 93 through 98 removed outlier: 6.638A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AF8, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AF9, first strand: chain 'f' and resid 10 through 19 removed outlier: 5.914A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA f 81 " --> pdb=" O HIS f 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG f 74 " --> pdb=" O ARG f 83 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG f 85 " --> pdb=" O ILE f 72 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE f 72 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.510A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'o' and resid 131 through 134 removed outlier: 4.169A pdb=" N ARG o 133 " --> pdb=" O GLU o 152 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL o 106 " --> pdb=" O ILE o 181 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.515A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'x' and resid 122 through 124 removed outlier: 5.296A pdb=" N ASN x 159 " --> pdb=" O LEU x 176 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER x 177 " --> pdb=" O MET x 272 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET x 272 " --> pdb=" O SER x 177 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU x 179 " --> pdb=" O PHE x 270 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE x 270 " --> pdb=" O LEU x 179 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'x' and resid 197 through 201 removed outlier: 6.113A pdb=" N LYS x 279 " --> pdb=" O VAL x 289 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL x 289 " --> pdb=" O LYS x 279 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'y' and resid 17 through 18 Processing sheet with id=AG7, first strand: chain 'y' and resid 71 through 73 removed outlier: 7.101A pdb=" N VAL y 72 " --> pdb=" O VAL y 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 2107 hydrogen bonds defined for protein. 5931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1203 hydrogen bonds 1932 hydrogen bond angles 0 basepair planarities 496 basepair parallelities 938 stacking parallelities Total time for adding SS restraints: 66.11 Time building geometry restraints manager: 33.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10186 1.32 - 1.44: 31565 1.44 - 1.57: 39921 1.57 - 1.69: 3207 1.69 - 1.82: 190 Bond restraints: 85069 Sorted by residual: bond pdb=" C VAL 3 11 " pdb=" O VAL 3 11 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" CA PRO L 60 " pdb=" C PRO L 60 " ideal model delta sigma weight residual 1.514 1.502 0.012 5.50e-03 3.31e+04 4.61e+00 bond pdb=" CB PRO S 19 " pdb=" CG PRO S 19 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.57e+00 bond pdb=" C ALA E 144 " pdb=" O ALA E 144 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 3.85e+00 bond pdb=" C MET B 323 " pdb=" O MET B 323 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.21e-02 6.83e+03 3.63e+00 ... (remaining 85064 not shown) Histogram of bond angle deviations from ideal: 96.39 - 103.97: 5814 103.97 - 111.55: 43985 111.55 - 119.13: 29485 119.13 - 126.71: 38570 126.71 - 134.28: 4969 Bond angle restraints: 122823 Sorted by residual: angle pdb=" CA PRO S 19 " pdb=" N PRO S 19 " pdb=" CD PRO S 19 " ideal model delta sigma weight residual 112.00 104.62 7.38 1.40e+00 5.10e-01 2.78e+01 angle pdb=" N LYS B 66 " pdb=" CA LYS B 66 " pdb=" C LYS B 66 " ideal model delta sigma weight residual 111.71 106.22 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" C4' U 6 72 " pdb=" C3' U 6 72 " pdb=" O3' U 6 72 " ideal model delta sigma weight residual 109.40 115.86 -6.46 1.50e+00 4.44e-01 1.85e+01 angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 125.57 -12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA LYS Y 124 " pdb=" CB LYS Y 124 " pdb=" CG LYS Y 124 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 ... (remaining 122818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 45599 35.67 - 71.33: 1970 71.33 - 107.00: 170 107.00 - 142.67: 26 142.67 - 178.33: 36 Dihedral angle restraints: 47801 sinusoidal: 29999 harmonic: 17802 Sorted by residual: dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual 200.00 23.09 176.91 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 11155 " pdb=" C1' U 11155 " pdb=" N1 U 11155 " pdb=" C2 U 11155 " ideal model delta sinusoidal sigma weight residual -160.00 14.33 -174.33 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 1 300 " pdb=" C1' U 1 300 " pdb=" N1 U 1 300 " pdb=" C2 U 1 300 " ideal model delta sinusoidal sigma weight residual 200.00 27.55 172.45 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 47798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 13279 0.050 - 0.100: 1474 0.100 - 0.151: 365 0.151 - 0.201: 71 0.201 - 0.251: 8 Chirality restraints: 15197 Sorted by residual: chirality pdb=" C3' G 1 505 " pdb=" C4' G 1 505 " pdb=" O3' G 1 505 " pdb=" C2' G 1 505 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' A 1 488 " pdb=" C4' A 1 488 " pdb=" O3' A 1 488 " pdb=" C2' A 1 488 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU B 356 " pdb=" CB LEU B 356 " pdb=" CD1 LEU B 356 " pdb=" CD2 LEU B 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 15194 not shown) Planarity restraints: 9740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU S 18 " 0.068 5.00e-02 4.00e+02 9.95e-02 1.59e+01 pdb=" N PRO S 19 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO S 19 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 19 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 414 " -0.036 2.00e-02 2.50e+03 1.52e-02 6.90e+00 pdb=" N9 G 1 414 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G 1 414 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 414 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 1 414 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 414 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G 1 414 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G 1 414 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 1 414 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 1 414 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 414 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G 1 414 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 106 " -0.019 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" CG TRP B 106 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 106 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 106 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 106 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 106 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 106 " -0.008 2.00e-02 2.50e+03 ... (remaining 9737 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6322 2.72 - 3.27: 76346 3.27 - 3.81: 158396 3.81 - 4.36: 198741 4.36 - 4.90: 283279 Nonbonded interactions: 723084 Sorted by model distance: nonbonded pdb=" N GLN o 120 " pdb=" OE1 GLN o 120 " model vdw 2.180 2.520 nonbonded pdb=" O THR C 215 " pdb=" OG1 THR C 215 " model vdw 2.193 2.440 nonbonded pdb=" O2' C 13156 " pdb=" O2' U 13433 " model vdw 2.198 2.440 nonbonded pdb=" N GLU E 152 " pdb=" OE1 GLU E 152 " model vdw 2.200 2.520 nonbonded pdb=" OG SER x 171 " pdb=" O GLY x 280 " model vdw 2.201 2.440 ... (remaining 723079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1619 5.49 5 S 116 5.16 5 C 44250 2.51 5 N 14804 2.21 5 O 19459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.04 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: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 30.600 Check model and map are aligned: 0.880 Convert atoms to be neutral: 0.530 Process input model: 233.070 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 284.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 85069 Z= 0.222 Angle : 0.511 12.873 122823 Z= 0.275 Chirality : 0.036 0.251 15197 Planarity : 0.004 0.100 9740 Dihedral : 17.436 178.331 36215 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.10 (0.11), residues: 5994 helix: 1.03 (0.11), residues: 2265 sheet: -0.38 (0.18), residues: 894 loop : -0.50 (0.12), residues: 2835 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 415 time to evaluate : 4.900 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 outliers start: 123 outliers final: 103 residues processed: 512 average time/residue: 1.5034 time to fit residues: 1038.2919 Evaluate side-chains 508 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 405 time to evaluate : 4.959 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 91 residues processed: 14 average time/residue: 1.0652 time to fit residues: 28.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 640 optimal weight: 1.9990 chunk 574 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 387 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 594 optimal weight: 50.0000 chunk 229 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 442 optimal weight: 20.0000 chunk 688 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 57 ASN 5 11 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN F 69 GLN G 107 GLN L 37 GLN L 40 GLN L 110 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN h 19 GLN i 93 GLN o 114 HIS o 147 HIS ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 85069 Z= 0.232 Angle : 0.577 12.608 122823 Z= 0.295 Chirality : 0.038 0.296 15197 Planarity : 0.004 0.069 9740 Dihedral : 16.297 179.634 25990 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.39 (0.11), residues: 5994 helix: 1.45 (0.11), residues: 2362 sheet: -0.41 (0.18), residues: 870 loop : -0.50 (0.12), residues: 2762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 430 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 127 residues processed: 602 average time/residue: 1.4723 time to fit residues: 1208.9589 Evaluate side-chains 545 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 418 time to evaluate : 4.943 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 103 residues processed: 25 average time/residue: 0.7813 time to fit residues: 38.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 382 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 572 optimal weight: 30.0000 chunk 468 optimal weight: 40.0000 chunk 189 optimal weight: 0.6980 chunk 689 optimal weight: 30.0000 chunk 744 optimal weight: 50.0000 chunk 614 optimal weight: 0.9980 chunk 683 optimal weight: 0.7980 chunk 235 optimal weight: 0.2980 chunk 553 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN 5 11 GLN 5 302 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN G 107 GLN L 40 GLN M 119 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN S 88 ASN o 147 HIS v 33 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 85069 Z= 0.201 Angle : 0.543 17.351 122823 Z= 0.278 Chirality : 0.037 0.297 15197 Planarity : 0.004 0.068 9740 Dihedral : 16.261 179.686 25990 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer Outliers : 5.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.47 (0.11), residues: 5994 helix: 1.57 (0.11), residues: 2386 sheet: -0.41 (0.18), residues: 870 loop : -0.52 (0.12), residues: 2738 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 430 time to evaluate : 5.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 237 outliers final: 136 residues processed: 618 average time/residue: 1.4614 time to fit residues: 1243.5226 Evaluate side-chains 541 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 405 time to evaluate : 5.002 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 118 residues processed: 20 average time/residue: 0.8215 time to fit residues: 32.9131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 681 optimal weight: 20.0000 chunk 518 optimal weight: 0.0770 chunk 357 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 329 optimal weight: 0.0010 chunk 463 optimal weight: 0.0370 chunk 692 optimal weight: 3.9990 chunk 732 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 655 optimal weight: 0.0870 chunk 197 optimal weight: 1.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 147 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 85069 Z= 0.135 Angle : 0.520 9.958 122823 Z= 0.266 Chirality : 0.035 0.288 15197 Planarity : 0.004 0.078 9740 Dihedral : 16.192 179.653 25990 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.61 (0.11), residues: 5994 helix: 1.74 (0.11), residues: 2381 sheet: -0.37 (0.18), residues: 864 loop : -0.47 (0.12), residues: 2749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 430 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 203 outliers final: 135 residues processed: 596 average time/residue: 1.4506 time to fit residues: 1186.1256 Evaluate side-chains 541 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 406 time to evaluate : 4.933 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 120 residues processed: 17 average time/residue: 0.8334 time to fit residues: 29.1550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 610 optimal weight: 2.9990 chunk 415 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 625 optimal weight: 0.3980 chunk 506 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 657 optimal weight: 0.0870 chunk 184 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 139 GLN 5 11 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN Y 90 ASN o 147 HIS ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 85069 Z= 0.140 Angle : 0.510 11.919 122823 Z= 0.261 Chirality : 0.035 0.275 15197 Planarity : 0.004 0.082 9740 Dihedral : 16.079 179.374 25990 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.29 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.71 (0.11), residues: 5994 helix: 1.83 (0.11), residues: 2390 sheet: -0.38 (0.18), residues: 867 loop : -0.41 (0.12), residues: 2737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 436 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 213 outliers final: 128 residues processed: 607 average time/residue: 1.5038 time to fit residues: 1251.9975 Evaluate side-chains 542 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 414 time to evaluate : 4.990 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 115 residues processed: 17 average time/residue: 0.9500 time to fit residues: 31.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 246 optimal weight: 10.0000 chunk 659 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 733 optimal weight: 0.3980 chunk 608 optimal weight: 3.9990 chunk 339 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN O 47 HIS ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN o 147 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 85069 Z= 0.278 Angle : 0.570 10.140 122823 Z= 0.291 Chirality : 0.039 0.330 15197 Planarity : 0.004 0.073 9740 Dihedral : 16.109 179.750 25990 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 95.99 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.61 (0.11), residues: 5994 helix: 1.73 (0.11), residues: 2382 sheet: -0.35 (0.18), residues: 875 loop : -0.47 (0.12), residues: 2737 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 415 time to evaluate : 5.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 143 residues processed: 583 average time/residue: 1.4770 time to fit residues: 1179.3863 Evaluate side-chains 547 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 404 time to evaluate : 4.980 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 127 residues processed: 18 average time/residue: 0.8288 time to fit residues: 30.5118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 707 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 417 optimal weight: 0.7980 chunk 535 optimal weight: 0.6980 chunk 414 optimal weight: 0.8980 chunk 617 optimal weight: 4.9990 chunk 409 optimal weight: 3.9990 chunk 730 optimal weight: 1.9990 chunk 457 optimal weight: 20.0000 chunk 445 optimal weight: 0.6980 chunk 337 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN M 119 GLN O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN o 147 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 85069 Z= 0.166 Angle : 0.535 12.064 122823 Z= 0.273 Chirality : 0.036 0.299 15197 Planarity : 0.004 0.096 9740 Dihedral : 16.081 179.390 25990 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer Outliers : 4.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.69 (0.11), residues: 5994 helix: 1.82 (0.11), residues: 2381 sheet: -0.30 (0.18), residues: 866 loop : -0.45 (0.12), residues: 2747 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 418 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 144 residues processed: 567 average time/residue: 1.6341 time to fit residues: 1271.5118 Evaluate side-chains 549 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 405 time to evaluate : 5.056 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 127 residues processed: 20 average time/residue: 1.1817 time to fit residues: 41.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 451 optimal weight: 6.9990 chunk 291 optimal weight: 50.0000 chunk 436 optimal weight: 0.0060 chunk 220 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 464 optimal weight: 50.0000 chunk 497 optimal weight: 0.5980 chunk 361 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 574 optimal weight: 50.0000 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN M 119 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN o 147 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.103 85069 Z= 0.445 Angle : 0.670 13.333 122823 Z= 0.339 Chirality : 0.044 0.346 15197 Planarity : 0.005 0.070 9740 Dihedral : 16.240 179.861 25990 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.39 (0.11), residues: 5994 helix: 1.50 (0.11), residues: 2361 sheet: -0.37 (0.18), residues: 871 loop : -0.57 (0.12), residues: 2762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 407 time to evaluate : 5.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 190 outliers final: 139 residues processed: 562 average time/residue: 1.5811 time to fit residues: 1221.3982 Evaluate side-chains 538 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 399 time to evaluate : 4.961 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 123 residues processed: 17 average time/residue: 0.7756 time to fit residues: 28.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 664 optimal weight: 0.4980 chunk 699 optimal weight: 0.2980 chunk 638 optimal weight: 8.9990 chunk 680 optimal weight: 5.9990 chunk 409 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 534 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 615 optimal weight: 0.7980 chunk 643 optimal weight: 0.9980 chunk 678 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN D 313 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN M 119 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 85069 Z= 0.159 Angle : 0.545 13.686 122823 Z= 0.277 Chirality : 0.036 0.296 15197 Planarity : 0.004 0.084 9740 Dihedral : 16.062 179.974 25990 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.39 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5994 helix: 1.76 (0.11), residues: 2378 sheet: -0.32 (0.18), residues: 864 loop : -0.50 (0.12), residues: 2752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 412 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 129 residues processed: 550 average time/residue: 1.5265 time to fit residues: 1150.1397 Evaluate side-chains 527 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 398 time to evaluate : 5.069 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 119 residues processed: 10 average time/residue: 0.7414 time to fit residues: 18.8584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 447 optimal weight: 20.0000 chunk 719 optimal weight: 0.7980 chunk 439 optimal weight: 50.0000 chunk 341 optimal weight: 5.9990 chunk 500 optimal weight: 0.6980 chunk 755 optimal weight: 50.0000 chunk 695 optimal weight: 1.9990 chunk 601 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 464 optimal weight: 50.0000 chunk 368 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 139 GLN ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN M 119 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 85069 Z= 0.390 Angle : 0.644 14.112 122823 Z= 0.327 Chirality : 0.042 0.345 15197 Planarity : 0.005 0.097 9740 Dihedral : 16.131 179.764 25990 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.43 (0.11), residues: 5994 helix: 1.56 (0.11), residues: 2365 sheet: -0.38 (0.18), residues: 885 loop : -0.57 (0.12), residues: 2744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 402 time to evaluate : 5.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 135 residues processed: 528 average time/residue: 1.5360 time to fit residues: 1111.8376 Evaluate side-chains 533 residues out of total 5290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 398 time to evaluate : 4.978 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 123 residues processed: 14 average time/residue: 0.8190 time to fit residues: 24.9013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 758 random chunks: chunk 477 optimal weight: 0.8980 chunk 640 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 554 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 602 optimal weight: 40.0000 chunk 252 optimal weight: 40.0000 chunk 618 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 107 GLN L 40 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146967 restraints weight = 131580.505| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.30 r_work: 0.3727 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 85069 Z= 0.149 Angle : 0.544 13.565 122823 Z= 0.277 Chirality : 0.036 0.288 15197 Planarity : 0.004 0.074 9740 Dihedral : 15.997 179.479 25990 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: 0.66 (0.11), residues: 5994 helix: 1.78 (0.11), residues: 2381 sheet: -0.27 (0.18), residues: 855 loop : -0.49 (0.12), residues: 2758 =============================================================================== Job complete usr+sys time: 18974.80 seconds wall clock time: 334 minutes 33.41 seconds (20073.41 seconds total)