Starting phenix.real_space_refine (version: dev) on Tue May 17 07:28:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryf_24738/05_2022/7ryf_24738_updated.pdb" } resolution = 2.65 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= 0.002 sd= 0.039 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 "1 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M ASP 117": "OD1" <-> "OD2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "P ASP 49": "OD1" <-> "OD2" Residue "P ASP 97": "OD1" <-> "OD2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 14": "OD1" <-> "OD2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 125": "OD1" <-> "OD2" Residue "b ASP 161": "OD1" <-> "OD2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "d TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d ASP 101": "OD1" <-> "OD2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 33": "OD1" <-> "OD2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 74": "OE1" <-> "OE2" Residue "h ASP 91": "OD1" <-> "OD2" Residue "i ASP 105": "OD1" <-> "OD2" Residue "m PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ASP 50": "OD1" <-> "OD2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 137516 Number of models: 1 Model: "" Number of chains: 55 Chain: "0" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 57610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2685, 57610 Classifications: {'RNA': 2685} Modifications used: {'rna3p': 9, 'rna2p': 3, 'rna3p_pur': 1289, 'rna3p_pyr': 990, 'rna2p_pur': 249, 'rna2p_pyr': 145} Link IDs: {'rna3p': 2288, 'rna2p': 396} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 4, 'rna3p_pur': 56, 'rna2p_pyr': 6} Link IDs: {'rna3p': 105, 'rna2p': 9} Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2104 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 16, 'TRANS': 254} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1566 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 4, 'TRANS': 204, 'PCIS': 1} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1117 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna3p': 8, 'rna2p_pyr': 85, 'rna3p_pur': 758, 'rna2p': 1, 'rna3p_pyr': 571, 'rna2p_pur': 105} Link IDs: {'rna3p': 1337, 'rna2p': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 94, 'PCIS': 1} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 115, 'PCIS': 1} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna3p': 4, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 29, 'rna2p_pur': 5} Link IDs: {'rna3p': 67, 'rna2p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna3p': 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 127 Unusual residues: {'80P': 3, ' MG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1355 SG CYS 3 11 179.654 122.169 137.208 1.00 35.24 S ATOM 1371 SG CYS 3 14 178.542 124.040 140.333 1.00 34.96 S ATOM 1476 SG CYS 3 27 180.053 125.954 137.426 1.00 35.78 S Time building chain proxies: 55.74, per 1000 atoms: 0.41 Number of scatterers: 137516 At special positions: 0 Unit cell: (227.601, 250.47, 278.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 140 16.00 P 4406 15.00 Mg 4 11.99 F 9 9.00 O 38330 8.00 N 25571 7.00 C 69055 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: 51.71 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10074 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 66 sheets defined 39.7% alpha, 18.7% beta 1376 base pairs and 2122 stacking pairs defined. Time for finding SS restraints: 57.48 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.132A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.606A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 45 removed outlier: 5.254A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.151A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.647A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.052A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.810A pdb=" N MET C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.165A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.156A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 5.221A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.627A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.834A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 4.027A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 5.849A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.905A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.402A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.593A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 3.807A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.406A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 112 removed outlier: 4.732A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 5.457A pdb=" N ARG F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.593A pdb=" N TRP G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR G 67 " --> pdb=" O MET G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.837A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.962A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.898A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.794A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.545A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.866A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.614A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.017A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.031A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 4.164A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.753A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.991A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 4.672A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.489A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 17 removed outlier: 4.007A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS O 17 " --> pdb=" O ASN O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.713A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.801A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.831A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.005A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.693A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.099A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.849A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.693A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.125A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.165A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.944A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 5.012A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.283A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.677A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.924A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 29 through 34 Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.938A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 78 through 90 Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.418A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 151 removed outlier: 3.757A pdb=" N LYS b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 228 removed outlier: 4.842A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.670A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 48 removed outlier: 5.220A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.607A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.293A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 removed outlier: 3.624A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.585A pdb=" N GLY c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.275A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 70 through 85 removed outlier: 3.521A pdb=" N ASN d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.009A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.473A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.243A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.558A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.676A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.980A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 54 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.662A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 148 Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 38 removed outlier: 4.377A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.589A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL i 45 " --> pdb=" O THR i 41 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 Processing helix chain 'i' and resid 92 through 100 removed outlier: 3.579A pdb=" N ALA i 99 " --> pdb=" O VAL i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.734A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 4.056A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 Processing helix chain 'k' and resid 58 through 77 removed outlier: 3.503A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.700A pdb=" N GLY k 100 " --> pdb=" O VAL k 96 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL k 102 " --> pdb=" O ALA k 98 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.735A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.530A pdb=" N LEU m 19 " --> pdb=" O ALA m 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.063A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.021A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.785A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.678A pdb=" N GLY m 111 " --> pdb=" O ARG m 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.691A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.791A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.751A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 removed outlier: 3.572A pdb=" N GLN p 81 " --> pdb=" O HIS p 77 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY p 82 " --> pdb=" O TRP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.013A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.008A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.249A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.512A pdb=" N LYS t 16 " --> pdb=" O ARG t 12 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.695A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.668A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 6.280A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.681A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 4.003A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.985A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N SER C 170 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.310A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.177A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.547A pdb=" N VAL D 85 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 26 through 29 Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.564A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.664A pdb=" N GLY E 41 " --> pdb=" O GLN E 89 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG E 43 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG E 87 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS E 45 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA E 85 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.180A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 86 through 92 removed outlier: 3.716A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR F 158 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLY F 126 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.244A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'H' and resid 1 through 5 removed outlier: 6.720A pdb=" N MET H 1 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER H 20 " --> pdb=" O MET H 1 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL H 3 " --> pdb=" O LYS H 18 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS H 18 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU H 5 " --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.270A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.198A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG J 64 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.956A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 122 through 125 Processing sheet with id= 26, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.649A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 31 through 37 removed outlier: 7.742A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= 29, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= 30, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.616A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.892A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.203A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.184A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 35, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.728A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 2 through 8 removed outlier: 5.017A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 11 through 14 removed outlier: 4.241A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.554A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN T 44 " --> pdb=" O GLY T 55 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY T 55 " --> pdb=" O GLN T 44 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 73 through 76 Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.752A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 42, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.520A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 44, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.310A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 28 through 31 removed outlier: 4.222A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.008A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 92 through 95 removed outlier: 3.696A pdb=" N PHE b 71 " --> pdb=" O PRO b 92 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 54 through 59 removed outlier: 4.031A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 164 through 170 Processing sheet with id= 50, first strand: chain 'd' and resid 142 through 146 removed outlier: 4.382A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE d 184 " --> pdb=" O ASP d 143 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.854A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 83 through 87 removed outlier: 5.355A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 42 removed outlier: 4.001A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.849A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 23 through 29 removed outlier: 5.965A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.434A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.812A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 42 through 53 removed outlier: 5.080A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 29 through 35 removed outlier: 3.679A pdb=" N ASN k 107 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.261A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG l 94 " --> pdb=" O GLY l 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 51 through 56 removed outlier: 4.876A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.780A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 7 through 12 removed outlier: 6.138A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 's' and resid 47 through 52 removed outlier: 4.860A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1855 hydrogen bonds defined for protein. 5487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3446 hydrogen bonds 5442 hydrogen bond angles 0 basepair planarities 1376 basepair parallelities 2122 stacking parallelities Total time for adding SS restraints: 246.06 Time building geometry restraints manager: 57.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12406 1.31 - 1.43: 66840 1.43 - 1.56: 61076 1.56 - 1.69: 8842 1.69 - 1.82: 249 Bond restraints: 149413 Sorted by residual: bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.805 1.448 0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" C4 5MU v 55 " pdb=" C5 5MU v 55 " ideal model delta sigma weight residual 1.805 1.450 0.355 2.00e-02 2.50e+03 3.16e+02 bond pdb=" C08 80P a1602 " pdb=" C09 80P a1602 " ideal model delta sigma weight residual 1.316 1.631 -0.315 2.00e-02 2.50e+03 2.48e+02 bond pdb=" C08 80P a1603 " pdb=" C09 80P a1603 " ideal model delta sigma weight residual 1.316 1.621 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C08 80P a1601 " pdb=" C09 80P a1601 " ideal model delta sigma weight residual 1.316 1.619 -0.303 2.00e-02 2.50e+03 2.30e+02 ... (remaining 149408 not shown) Histogram of bond angle deviations from ideal: 98.21 - 107.80: 33733 107.80 - 117.39: 103568 117.39 - 126.98: 75304 126.98 - 136.57: 10967 136.57 - 146.17: 4 Bond angle restraints: 223576 Sorted by residual: angle pdb=" C1' 2MA A2499 " pdb=" N9 2MA A2499 " pdb=" C4 2MA A2499 " ideal model delta sigma weight residual 103.49 138.73 -35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C1' 2MA A2499 " pdb=" N9 2MA A2499 " pdb=" C8 2MA A2499 " ideal model delta sigma weight residual 144.94 110.49 34.45 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C16 80P a1601 " pdb=" C17 80P a1601 " pdb=" C18 80P a1601 " ideal model delta sigma weight residual 95.49 127.57 -32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C16 80P a1603 " pdb=" C17 80P a1603 " pdb=" C18 80P a1603 " ideal model delta sigma weight residual 95.49 127.06 -31.57 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C16 80P a1602 " pdb=" C17 80P a1602 " pdb=" C18 80P a1602 " ideal model delta sigma weight residual 95.49 126.64 -31.15 3.00e+00 1.11e-01 1.08e+02 ... (remaining 223571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 77054 35.89 - 71.77: 2338 71.77 - 107.66: 203 107.66 - 143.55: 37 143.55 - 179.44: 75 Dihedral angle restraints: 79707 sinusoidal: 64065 harmonic: 15642 Sorted by residual: dihedral pdb=" O4' C a 178 " pdb=" C1' C a 178 " pdb=" N1 C a 178 " pdb=" C2 C a 178 " ideal model delta sinusoidal sigma weight residual 200.00 23.16 176.84 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2550 " pdb=" C1' U A2550 " pdb=" N1 U A2550 " pdb=" C2 U A2550 " ideal model delta sinusoidal sigma weight residual -160.00 16.51 -176.51 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual 200.00 31.65 168.35 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 79704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.126: 28554 1.126 - 2.253: 0 2.253 - 3.379: 0 3.379 - 4.506: 0 4.506 - 5.632: 3 Chirality restraints: 28557 Sorted by residual: chirality pdb=" C08 80P a1602 " pdb=" C07 80P a1602 " pdb=" C09 80P a1602 " pdb=" C21 80P a1602 " both_signs ideal model delta sigma weight residual False 2.49 -3.14 5.63 2.00e-01 2.50e+01 7.93e+02 chirality pdb=" C08 80P a1603 " pdb=" C07 80P a1603 " pdb=" C09 80P a1603 " pdb=" C21 80P a1603 " both_signs ideal model delta sigma weight residual False 2.49 -3.12 5.61 2.00e-01 2.50e+01 7.86e+02 chirality pdb=" C08 80P a1601 " pdb=" C07 80P a1601 " pdb=" C09 80P a1601 " pdb=" C21 80P a1601 " both_signs ideal model delta sigma weight residual False 2.49 -3.07 5.56 2.00e-01 2.50e+01 7.73e+02 ... (remaining 28554 not shown) Planarity restraints: 11968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.074 2.00e-02 2.50e+03 6.19e-01 8.62e+03 pdb=" C4' 7MG A2065 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.660 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.599 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.671 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.166 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 1.006 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.210 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.958 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " -0.048 2.00e-02 2.50e+03 5.94e-01 7.95e+03 pdb=" C4' 7MG a 524 " -0.441 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " -0.664 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " 0.609 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " 0.196 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " -0.945 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " -0.216 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " 0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.052 2.00e-02 2.50e+03 5.73e-01 7.39e+03 pdb=" C4' 2MG a1204 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.590 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.593 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.195 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.942 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.230 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.861 2.00e-02 2.50e+03 ... (remaining 11965 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 268 2.39 - 3.02: 70848 3.02 - 3.65: 234371 3.65 - 4.27: 389037 4.27 - 4.90: 525764 Nonbonded interactions: 1220288 Sorted by model distance: nonbonded pdb=" O2' C a1025 " pdb=" O5' U a1026 " model vdw 1.764 2.440 nonbonded pdb=" O2' G a 572 " pdb=" OP2 G a 818 " model vdw 1.866 2.440 nonbonded pdb=" OP1 A a1194 " pdb="MG MG a1605 " model vdw 1.875 2.170 nonbonded pdb=" OG SER G 80 " pdb=" OE1 GLU G 81 " model vdw 1.902 2.440 nonbonded pdb=" O2' G A1880 " pdb=" OP1 A A1881 " model vdw 1.908 2.440 ... (remaining 1220283 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4406 5.49 5 Mg 4 5.21 5 S 140 5.16 5 C 69055 2.51 5 N 25571 2.21 5 O 38330 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.610 Construct map_model_manager: 0.070 Extract box with map and model: 35.700 Check model and map are aligned: 1.520 Convert atoms to be neutral: 0.920 Process input model: 537.100 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 601.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.006 0.357 149413 Z= 0.356 Angle : 0.623 35.239 223576 Z= 0.315 Chirality : 0.067 5.632 28557 Planarity : 0.016 0.619 11968 Dihedral : 15.085 179.436 69633 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 5399 helix: 1.95 (0.12), residues: 1883 sheet: 0.58 (0.15), residues: 1053 loop : -0.19 (0.12), residues: 2463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1205 time to evaluate : 5.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1205 average time/residue: 2.2929 time to fit residues: 3913.1842 Evaluate side-chains 1075 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1074 time to evaluate : 5.937 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.0048 time to fit residues: 8.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 9.9990 chunk 732 optimal weight: 9.9990 chunk 406 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 494 optimal weight: 0.9990 chunk 391 optimal weight: 10.0000 chunk 757 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 460 optimal weight: 4.9990 chunk 564 optimal weight: 9.9990 chunk 878 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 33 ASN D 37 GLN D 153 GLN E 40 GLN E 93 GLN E 96 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN K 18 HIS K 101 ASN M 72 ASN O 55 ASN O 78 GLN P 52 GLN P 101 HIS Q 69 HIS Q 87 GLN R 40 ASN V 35 ASN V 40 GLN W 36 HIS Z 25 ASN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 HIS c 100 GLN c 104 ASN c 123 GLN c 140 ASN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN i 30 ASN j 99 GLN k 117 HIS m 28 HIS n 33 ASN s 57 HIS s 69 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.103 149413 Z= 0.464 Angle : 0.938 25.696 223576 Z= 0.467 Chirality : 0.055 2.537 28557 Planarity : 0.008 0.140 11968 Dihedral : 15.599 179.749 58934 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.81 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 5399 helix: 1.19 (0.12), residues: 1882 sheet: 0.33 (0.15), residues: 1056 loop : -0.47 (0.12), residues: 2461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1080 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 100 residues processed: 1126 average time/residue: 2.2601 time to fit residues: 3591.5559 Evaluate side-chains 1161 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1061 time to evaluate : 5.491 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 33 residues processed: 67 average time/residue: 1.4173 time to fit residues: 162.0659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 730 optimal weight: 3.9990 chunk 597 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 879 optimal weight: 4.9990 chunk 950 optimal weight: 0.7980 chunk 783 optimal weight: 0.6980 chunk 872 optimal weight: 30.0000 chunk 299 optimal weight: 3.9990 chunk 705 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN C 70 ASN C 134 ASN D 37 GLN E 40 GLN E 96 ASN E 162 ASN I 61 GLN K 18 HIS M 72 ASN O 55 ASN P 52 GLN W 16 ASN W 32 ASN W 36 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN c 100 GLN c 123 GLN h 86 GLN i 30 ASN i 124 GLN o 61 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 149413 Z= 0.234 Angle : 0.717 23.899 223576 Z= 0.372 Chirality : 0.045 2.169 28557 Planarity : 0.006 0.130 11968 Dihedral : 15.150 179.432 58934 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5399 helix: 1.47 (0.12), residues: 1885 sheet: 0.34 (0.15), residues: 1086 loop : -0.44 (0.12), residues: 2428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1072 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 102 residues processed: 1147 average time/residue: 2.3065 time to fit residues: 3732.1010 Evaluate side-chains 1150 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1048 time to evaluate : 5.945 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 48 residues processed: 54 average time/residue: 1.3013 time to fit residues: 127.7312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 8.9990 chunk 661 optimal weight: 3.9990 chunk 456 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 419 optimal weight: 2.9990 chunk 590 optimal weight: 3.9990 chunk 882 optimal weight: 7.9990 chunk 934 optimal weight: 0.9980 chunk 461 optimal weight: 4.9990 chunk 836 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 HIS C 70 ASN C 198 GLN D 37 GLN E 40 GLN E 162 ASN K 18 HIS M 72 ASN O 9 GLN O 55 ASN P 52 GLN W 32 ASN W 36 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS h 86 GLN i 30 ASN i 124 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 149413 Z= 0.356 Angle : 0.829 24.786 223576 Z= 0.419 Chirality : 0.049 2.247 28557 Planarity : 0.007 0.137 11968 Dihedral : 15.358 179.892 58934 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % 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: 0.28 (0.11), residues: 5399 helix: 1.22 (0.12), residues: 1875 sheet: 0.23 (0.15), residues: 1080 loop : -0.59 (0.12), residues: 2444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1050 time to evaluate : 5.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 141 residues processed: 1130 average time/residue: 2.2668 time to fit residues: 3628.7281 Evaluate side-chains 1180 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1039 time to evaluate : 5.375 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 58 residues processed: 85 average time/residue: 1.3468 time to fit residues: 194.5861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 0.0670 chunk 530 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 695 optimal weight: 40.0000 chunk 385 optimal weight: 30.0000 chunk 797 optimal weight: 0.9980 chunk 646 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 477 optimal weight: 0.5980 chunk 838 optimal weight: 0.6980 chunk 235 optimal weight: 7.9990 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 134 ASN C 185 HIS D 37 GLN E 40 GLN E 162 ASN K 18 HIS M 72 ASN N 99 HIS O 55 ASN P 52 GLN V 40 GLN W 32 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN j 99 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 149413 Z= 0.205 Angle : 0.691 23.813 223576 Z= 0.359 Chirality : 0.043 2.125 28557 Planarity : 0.006 0.128 11968 Dihedral : 15.002 179.982 58934 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5399 helix: 1.58 (0.12), residues: 1874 sheet: 0.29 (0.15), residues: 1089 loop : -0.52 (0.12), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1051 time to evaluate : 5.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 122 residues processed: 1146 average time/residue: 2.2915 time to fit residues: 3720.9101 Evaluate side-chains 1160 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1038 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 69 residues processed: 54 average time/residue: 1.4555 time to fit residues: 137.5965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 0.5980 chunk 841 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 548 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 935 optimal weight: 1.9990 chunk 776 optimal weight: 10.0000 chunk 433 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 491 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN D 37 GLN E 40 GLN E 162 ASN K 18 HIS M 72 ASN O 55 ASN P 52 GLN W 32 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 100 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 149413 Z= 0.237 Angle : 0.716 24.199 223576 Z= 0.368 Chirality : 0.044 2.157 28557 Planarity : 0.006 0.131 11968 Dihedral : 14.994 179.944 58934 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.51 (0.11), residues: 5399 helix: 1.53 (0.12), residues: 1877 sheet: 0.27 (0.15), residues: 1072 loop : -0.52 (0.12), residues: 2450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1037 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 129 residues processed: 1123 average time/residue: 2.3348 time to fit residues: 3746.8668 Evaluate side-chains 1155 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1026 time to evaluate : 5.933 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 69 residues processed: 60 average time/residue: 1.5078 time to fit residues: 154.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 533 optimal weight: 0.0010 chunk 683 optimal weight: 2.9990 chunk 529 optimal weight: 8.9990 chunk 787 optimal weight: 2.9990 chunk 522 optimal weight: 0.0040 chunk 932 optimal weight: 0.7980 chunk 583 optimal weight: 3.9990 chunk 568 optimal weight: 6.9990 chunk 430 optimal weight: 0.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN D 37 GLN E 40 GLN E 96 ASN E 162 ASN K 18 HIS M 72 ASN O 55 ASN P 52 GLN S 3 ASN W 32 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN b 170 HIS c 100 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN j 99 GLN n 8 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 149413 Z= 0.124 Angle : 0.628 23.764 223576 Z= 0.328 Chirality : 0.040 2.035 28557 Planarity : 0.005 0.122 11968 Dihedral : 14.694 179.712 58934 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.79 (0.11), residues: 5399 helix: 1.84 (0.12), residues: 1881 sheet: 0.38 (0.16), residues: 1080 loop : -0.41 (0.12), residues: 2438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1051 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 149 outliers final: 103 residues processed: 1138 average time/residue: 2.2715 time to fit residues: 3672.5419 Evaluate side-chains 1130 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1027 time to evaluate : 5.934 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 70 residues processed: 33 average time/residue: 1.4110 time to fit residues: 84.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 6.9990 chunk 372 optimal weight: 50.0000 chunk 556 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 634 optimal weight: 3.9990 chunk 460 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 732 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN D 37 GLN D 47 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS L 46 GLN M 72 ASN O 55 ASN P 52 GLN S 2 ASN W 32 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN c 100 GLN g 32 GLN ** h 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN n 8 ASN p 62 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.139 149413 Z= 0.594 Angle : 1.035 25.305 223576 Z= 0.503 Chirality : 0.059 2.301 28557 Planarity : 0.009 0.145 11968 Dihedral : 15.497 179.825 58934 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer Outliers : 4.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % 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: -0.01 (0.11), residues: 5399 helix: 0.94 (0.12), residues: 1875 sheet: 0.10 (0.16), residues: 1064 loop : -0.73 (0.12), residues: 2460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1042 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 193 outliers final: 137 residues processed: 1134 average time/residue: 2.3165 time to fit residues: 3725.5735 Evaluate side-chains 1167 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1030 time to evaluate : 5.300 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 76 residues processed: 61 average time/residue: 1.4900 time to fit residues: 154.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 1.9990 chunk 892 optimal weight: 0.8980 chunk 814 optimal weight: 7.9990 chunk 868 optimal weight: 9.9990 chunk 522 optimal weight: 0.8980 chunk 378 optimal weight: 8.9990 chunk 682 optimal weight: 40.0000 chunk 266 optimal weight: 3.9990 chunk 784 optimal weight: 0.7980 chunk 821 optimal weight: 0.5980 chunk 865 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 260 ASN D 37 GLN E 162 ASN K 18 HIS L 46 GLN M 72 ASN O 55 ASN P 52 GLN V 40 GLN W 32 ASN b 57 ASN b 61 GLN c 100 GLN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN j 99 GLN n 8 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 149413 Z= 0.142 Angle : 0.659 23.691 223576 Z= 0.343 Chirality : 0.041 2.048 28557 Planarity : 0.006 0.124 11968 Dihedral : 14.820 179.875 58934 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.35 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.56 (0.11), residues: 5399 helix: 1.59 (0.12), residues: 1880 sheet: 0.28 (0.16), residues: 1069 loop : -0.51 (0.12), residues: 2450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1037 time to evaluate : 5.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 119 outliers final: 93 residues processed: 1115 average time/residue: 2.2598 time to fit residues: 3580.5196 Evaluate side-chains 1120 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1027 time to evaluate : 5.915 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 70 residues processed: 23 average time/residue: 1.6700 time to fit residues: 66.6796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 5.9990 chunk 918 optimal weight: 3.9990 chunk 560 optimal weight: 0.6980 chunk 435 optimal weight: 3.9990 chunk 638 optimal weight: 3.9990 chunk 963 optimal weight: 5.9990 chunk 886 optimal weight: 2.9990 chunk 767 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 592 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 198 GLN D 37 GLN K 18 HIS L 46 GLN M 72 ASN O 55 ASN P 52 GLN W 32 ASN c 28 GLN c 100 GLN ** h 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 86 GLN i 30 ASN i 124 GLN n 8 ASN o 40 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 149413 Z= 0.348 Angle : 0.810 24.530 223576 Z= 0.408 Chirality : 0.048 2.219 28557 Planarity : 0.007 0.136 11968 Dihedral : 15.092 179.869 58934 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.59 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 5399 helix: 1.31 (0.12), residues: 1879 sheet: 0.17 (0.16), residues: 1072 loop : -0.61 (0.12), residues: 2448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10798 Ramachandran restraints generated. 5399 Oldfield, 0 Emsley, 5399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1033 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 95 residues processed: 1108 average time/residue: 2.2892 time to fit residues: 3589.9077 Evaluate side-chains 1124 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1029 time to evaluate : 5.893 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 69 residues processed: 27 average time/residue: 1.5867 time to fit residues: 75.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 2.9990 chunk 817 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 707 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 768 optimal weight: 0.7980 chunk 321 optimal weight: 1.9990 chunk 788 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN C 198 GLN D 37 GLN K 18 HIS L 46 GLN M 72 ASN O 55 ASN P 52 GLN U 75 ASN W 32 ASN c 28 GLN c 100 GLN ** h 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN i 30 ASN i 124 GLN j 99 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151897 restraints weight = 168789.792| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.80 r_work: 0.3664 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.3570 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work: 0.3494 rms_B_bonded: 3.60 restraints_weight: 0.0625 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 149413 Z= 0.377 Angle : 0.841 24.313 223576 Z= 0.423 Chirality : 0.050 2.219 28557 Planarity : 0.007 0.137 11968 Dihedral : 15.206 179.950 58934 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.70 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % 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: 0.11 (0.11), residues: 5399 helix: 1.14 (0.12), residues: 1870 sheet: 0.07 (0.16), residues: 1067 loop : -0.71 (0.12), residues: 2462 =============================================================================== Job complete usr+sys time: 46216.88 seconds wall clock time: 791 minutes 37.19 seconds (47497.19 seconds total)