Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 19:17:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/10_2023/7m4z_23671_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4372 5.49 5 Mg 187 5.21 5 S 142 5.16 5 C 69334 2.51 5 N 25630 2.21 5 O 38504 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "K PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O ASP 94": "OD1" <-> "OD2" Residue "P ASP 102": "OD1" <-> "OD2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "Y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 35": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 92": "OD1" <-> "OD2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "p ASP 47": "OD1" <-> "OD2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "v ASP 55": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 138172 Number of models: 1 Model: "" Number of chains: 70 Chain: "0" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} 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: 58566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2730, 58566 Classifications: {'RNA': 2730} Modifications used: {'rna2p': 3, 'rna2p_pur': 247, 'rna2p_pyr': 145, 'rna3p': 12, 'rna3p_pur': 1313, 'rna3p_pyr': 1010} Link IDs: {'rna2p': 394, 'rna3p': 2335} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 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: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 9, 'rna3p': 105} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1566 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 204} 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: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} 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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 585 Classifications: {'peptide': 77} Modifications used: {'COO': 1} 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: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} 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, 'rna2p': 1, 'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p': 8, 'rna3p_pur': 751, 'rna3p_pyr': 571} Link IDs: {'rna2p': 197, 'rna3p': 1330} 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: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} 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: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} 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: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} 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: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 824 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} 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: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 215 Unusual residues: {' MG': 135, 'YQM': 2} Classifications: {'undetermined': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Unusual residues: {' MG': 48} Classifications: {'undetermined': 48} Link IDs: {None: 47} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1364 SG CYS 3 11 181.763 113.095 137.277 1.00 27.52 S ATOM 1380 SG CYS 3 14 180.673 114.656 140.592 1.00 26.86 S ATOM 1485 SG CYS 3 27 182.092 116.821 137.799 1.00 27.50 S Time building chain proxies: 49.36, per 1000 atoms: 0.36 Number of scatterers: 138172 At special positions: 0 Unit cell: (230.656, 245.072, 275.6, 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 142 16.00 P 4372 15.00 Mg 187 11.99 F 2 9.00 O 38504 8.00 N 25630 7.00 C 69334 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: 55.86 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal 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 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10316 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 71 sheets defined 39.3% alpha, 20.1% beta 1388 base pairs and 2110 stacking pairs defined. Time for finding SS restraints: 67.44 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.041A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.388A 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 Processing helix chain '2' and resid 36 through 44 removed outlier: 3.867A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.901A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.404A 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 30 through 35 removed outlier: 3.710A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.406A 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: 3.809A 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: 3.908A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.025A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.271A 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: 4.480A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.532A 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 'D' and resid 57 through 62 removed outlier: 3.659A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.129A 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 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.800A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.520A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.948A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 6.456A pdb=" N GLU F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.678A 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 111 removed outlier: 5.240A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.315A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' 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: 3.740A pdb=" N TRP G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.863A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.146A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 3.693A pdb=" N VAL I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN I 12 " --> pdb=" O PRO I 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 12' Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.769A 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 removed outlier: 3.794A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.698A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.668A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 4.445A pdb=" N ARG J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 108' Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.847A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.456A 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 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.711A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.983A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 85' 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 removed outlier: 4.307A pdb=" N ARG L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.734A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.929A 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 57 removed outlier: 3.648A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.413A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.854A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.801A 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: 3.565A pdb=" N LYS N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.425A 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 16 removed outlier: 4.038A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.404A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 22 Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.772A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.719A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.088A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.946A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.298A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.424A 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: 3.893A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.290A 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: 5.014A 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 57 removed outlier: 4.071A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 4.471A pdb=" N GLU U 62 " --> pdb=" O ASN U 58 " (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: 5.099A 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: 4.079A 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: 3.587A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 18 Processing helix chain 'b' and resid 7 through 15 removed outlier: 7.151A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.331A pdb=" N ILE b 33 " --> pdb=" O MET b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 4.026A 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 105 through 126 removed outlier: 4.652A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG b 110 " --> pdb=" O TRP b 106 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 150 Processing helix chain 'b' and resid 152 through 157 removed outlier: 4.595A pdb=" N MET b 156 " --> pdb=" O GLY b 152 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 152 through 157' Processing helix chain 'b' and resid 167 through 172 removed outlier: 3.608A pdb=" N GLU b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA b 172 " --> pdb=" O VAL b 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 167 through 172' Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 226 removed outlier: 4.163A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.020A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.011A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.904A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.937A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.252A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.592A 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 Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.545A pdb=" N LYS c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.440A 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 removed outlier: 3.546A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.097A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.521A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 removed outlier: 3.547A pdb=" N GLY d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.656A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 4.290A 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: 4.279A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.360A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.640A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 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: 3.658A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 4.659A 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 55 removed outlier: 3.564A pdb=" N LYS g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 5.225A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.587A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) 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 37 Processing helix chain 'i' and resid 39 through 54 Proline residue: i 49 - end of helix removed outlier: 3.589A pdb=" N LEU i 53 " --> pdb=" O PRO i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.937A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.781A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.944A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.339A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 4.287A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.120A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.497A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.910A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.938A 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: 3.818A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.866A 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: 3.740A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.170A 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 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 33 removed outlier: 5.109A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.782A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) 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: 4.119A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.615A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.193A 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 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.911A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.616A 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: 4.036A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.462A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.185A 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 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: 3.931A 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 38 removed outlier: 3.547A pdb=" N VAL u 32 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS u 34 " --> pdb=" O ALA u 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG u 35 " --> pdb=" O ASP u 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 28 through 38' Processing helix chain 'u' and resid 40 through 64 Processing helix chain 'v' and resid 14 through 30 Processing helix chain 'v' and resid 78 through 102 Processing sheet with id= 1, first strand: chain '0' and resid 2 through 9 removed outlier: 5.819A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 30 through 35 removed outlier: 5.951A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain '3' and resid 13 through 19 removed outlier: 8.274A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.236A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.882A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.742A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 164 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.386A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.064A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.521A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 35 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 111 through 117 removed outlier: 4.164A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 13, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.700A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.483A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.873A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 85 through 92 removed outlier: 5.021A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 19, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 20, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.809A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 22, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.748A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.556A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.083A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.970A pdb=" N ARG J 17 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.940A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 122 through 125 removed outlier: 3.546A pdb=" N LYS K 143 " --> pdb=" O PHE K 122 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.297A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.891A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.233A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= 32, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.767A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.996A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.239A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.339A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 37, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.050A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 39, first strand: chain 'S' and resid 11 through 14 removed outlier: 6.545A pdb=" N GLY S 27 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG S 76 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.430A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY T 55 " --> pdb=" O GLN T 44 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 8 through 11 Processing sheet with id= 42, first strand: chain 'U' and resid 65 through 68 Processing sheet with id= 43, first strand: chain 'V' and resid 34 through 37 removed outlier: 3.988A pdb=" N ASN V 35 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.588A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.319A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Y' and resid 32 through 39 removed outlier: 4.292A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS Y 2 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 28 through 31 removed outlier: 4.009A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 92 through 95 removed outlier: 3.736A pdb=" N ILE b 166 " --> pdb=" O VAL b 72 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.739A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.617A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 143 through 147 removed outlier: 3.853A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU d 181 " --> pdb=" O ASP d 176 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.863A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.816A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 55, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.803A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.723A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 73 through 79 removed outlier: 3.792A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.824A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 75 through 78 removed outlier: 5.026A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.072A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 35 through 38 removed outlier: 3.720A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.605A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.124A pdb=" N SER k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 34 removed outlier: 4.140A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 35 through 42 removed outlier: 5.702A pdb=" N ALA l 48 " --> pdb=" O PRO l 42 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.668A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 8 through 12 Processing sheet with id= 69, first strand: chain 'q' and resid 20 through 32 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 30 through 34 removed outlier: 4.103A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 1 through 7 removed outlier: 3.834A pdb=" N HIS v 38 " --> pdb=" O ARG v 63 " (cutoff:3.500A) 1931 hydrogen bonds defined for protein. 5727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3476 hydrogen bonds 5448 hydrogen bond angles 0 basepair planarities 1388 basepair parallelities 2110 stacking parallelities Total time for adding SS restraints: 209.83 Time building geometry restraints manager: 60.47 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: 13757 1.31 - 1.44: 65572 1.44 - 1.57: 61245 1.57 - 1.70: 8760 1.70 - 1.82: 254 Bond restraints: 149588 Sorted by residual: bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.575 -0.540 2.00e-02 2.50e+03 7.28e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.568 -0.533 2.00e-02 2.50e+03 7.11e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.547 0.404 2.00e-02 2.50e+03 4.08e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.951 1.570 0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C15 YQM A3202 " pdb=" C16 YQM A3202 " ideal model delta sigma weight residual 1.771 1.409 0.362 2.00e-02 2.50e+03 3.28e+02 ... (remaining 149583 not shown) Histogram of bond angle deviations from ideal: 90.16 - 101.52: 1763 101.52 - 112.87: 107885 112.87 - 124.23: 94796 124.23 - 135.58: 19172 135.58 - 146.94: 4 Bond angle restraints: 223620 Sorted by residual: angle pdb=" N PRO l 122 " pdb=" CD PRO l 122 " pdb=" CG PRO l 122 " ideal model delta sigma weight residual 103.20 90.16 13.04 1.50e+00 4.44e-01 7.55e+01 angle pdb=" CA PRO l 122 " pdb=" N PRO l 122 " pdb=" CD PRO l 122 " ideal model delta sigma weight residual 112.00 100.67 11.33 1.40e+00 5.10e-01 6.55e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.94 -20.71 3.00e+00 1.11e-01 4.77e+01 angle pdb=" C1' 2MG A2441 " pdb=" N9 2MG A2441 " pdb=" C8 2MG A2441 " ideal model delta sigma weight residual 110.07 128.73 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.33 -18.26 3.00e+00 1.11e-01 3.70e+01 ... (remaining 223615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 77169 35.97 - 71.94: 2491 71.94 - 107.91: 186 107.91 - 143.88: 26 143.88 - 179.86: 69 Dihedral angle restraints: 79941 sinusoidal: 63927 harmonic: 16014 Sorted by residual: dihedral pdb=" O4' U a 205 " pdb=" C1' U a 205 " pdb=" N1 U a 205 " pdb=" C2 U a 205 " ideal model delta sinusoidal sigma weight residual 200.00 20.41 179.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2796 " pdb=" C1' U A2796 " pdb=" N1 U A2796 " pdb=" C2 U A2796 " ideal model delta sinusoidal sigma weight residual 200.00 22.12 177.88 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 22.32 177.68 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 79938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 27469 0.081 - 0.162: 1034 0.162 - 0.242: 25 0.242 - 0.323: 3 0.323 - 0.404: 6 Chirality restraints: 28537 Sorted by residual: chirality pdb=" C1* PSU A2576 " pdb=" O4* PSU A2576 " pdb=" C2* PSU A2576 " pdb=" C5 PSU A2576 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C19 YQM A3202 " pdb=" C05 YQM A3202 " pdb=" C17 YQM A3202 " pdb=" C20 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.71 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 28534 not shown) Planarity restraints: 12110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.057 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' 7MG A2065 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.671 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.634 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.187 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.966 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.213 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.048 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG a1204 " 0.452 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.679 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.615 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.940 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.211 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.924 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 963 " 0.008 2.00e-02 2.50e+03 5.71e-01 7.33e+03 pdb=" C4' 2MG a 963 " 0.441 2.00e-02 2.50e+03 pdb=" O4' 2MG a 963 " 0.712 2.00e-02 2.50e+03 pdb=" C3' 2MG a 963 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG a 963 " -0.528 2.00e-02 2.50e+03 pdb=" C2' 2MG a 963 " -0.243 2.00e-02 2.50e+03 pdb=" O2' 2MG a 963 " 0.858 2.00e-02 2.50e+03 pdb=" C1' 2MG a 963 " 0.214 2.00e-02 2.50e+03 pdb=" N9 2MG a 963 " -0.877 2.00e-02 2.50e+03 ... (remaining 12107 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 801 2.45 - 3.06: 80311 3.06 - 3.67: 246708 3.67 - 4.29: 386705 4.29 - 4.90: 524292 Nonbonded interactions: 1238817 Sorted by model distance: nonbonded pdb="MG MG a1631 " pdb=" O HOH a1702 " model vdw 1.833 2.170 nonbonded pdb="MG MG A3218 " pdb=" O HOH A3416 " model vdw 1.836 2.170 nonbonded pdb="MG MG a1641 " pdb=" O HOH a1722 " model vdw 1.838 2.170 nonbonded pdb="MG MG a1618 " pdb=" O HOH a1706 " model vdw 1.854 2.170 nonbonded pdb="MG MG a1641 " pdb=" O HOH a1719 " model vdw 1.857 2.170 ... (remaining 1238812 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 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.590 Construct map_model_manager: 0.080 Extract box with map and model: 29.530 Check model and map are aligned: 1.520 Set scattering table: 0.910 Process input model: 494.840 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 544.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.540 149588 Z= 0.312 Angle : 0.545 20.710 223620 Z= 0.290 Chirality : 0.034 0.404 28537 Planarity : 0.016 0.605 12110 Dihedral : 15.139 179.855 69625 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 1.09 (0.11), residues: 5527 helix: 2.17 (0.12), residues: 1885 sheet: 0.66 (0.15), residues: 1153 loop : -0.35 (0.12), residues: 2489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1094 time to evaluate : 5.685 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 outliers start: 0 outliers final: 2 residues processed: 1094 average time/residue: 2.2439 time to fit residues: 3424.4093 Evaluate side-chains 986 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 984 time to evaluate : 5.729 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.0876 time to fit residues: 10.1391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 825 optimal weight: 0.0770 chunk 741 optimal weight: 40.0000 chunk 411 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 500 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 766 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 466 optimal weight: 2.9990 chunk 570 optimal weight: 9.9990 chunk 888 optimal weight: 7.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 4 GLN 3 35 GLN 3 37 GLN C 86 ASN C 90 HIS C 120 ASN C 185 HIS C 201 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 153 GLN D 167 HIS E 40 GLN I 58 ASN I 136 GLN J 3 GLN J 82 ASN M 5 ASN M 23 ASN O 44 GLN P 37 GLN Q 12 HIS Q 82 HIS R 37 ASN T 47 ASN U 84 HIS W 17 ASN Z 25 ASN Z 37 HIS c 21 ASN c 25 ASN c 49 ASN e 88 HIS f 3 HIS h 4 GLN h 41 GLN h 86 GLN i 79 HIS k 23 HIS m 105 ASN o 40 GLN r 52 GLN s 83 HIS t 3 ASN t 20 HIS v 13 ASN v 32 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 149588 Z= 0.447 Angle : 0.852 18.215 223620 Z= 0.430 Chirality : 0.049 0.459 28537 Planarity : 0.007 0.135 12110 Dihedral : 15.605 179.862 58656 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 3.16 % Allowed : 11.68 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.11), residues: 5527 helix: 1.43 (0.12), residues: 1884 sheet: 0.54 (0.15), residues: 1089 loop : -0.66 (0.11), residues: 2554 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1000 time to evaluate : 5.807 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: 145 outliers final: 69 residues processed: 1050 average time/residue: 2.2740 time to fit residues: 3329.9730 Evaluate side-chains 1028 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 959 time to evaluate : 5.759 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 25 residues processed: 44 average time/residue: 1.3422 time to fit residues: 103.1801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 493 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 739 optimal weight: 20.0000 chunk 604 optimal weight: 50.0000 chunk 244 optimal weight: 4.9990 chunk 889 optimal weight: 0.5980 chunk 961 optimal weight: 0.9980 chunk 792 optimal weight: 1.9990 chunk 882 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 713 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN D 33 ASN E 40 GLN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN d 148 HIS e 85 ASN h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN p 44 ASN p 84 GLN r 52 GLN t 3 ASN v 13 ASN v 78 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 149588 Z= 0.221 Angle : 0.652 15.336 223620 Z= 0.346 Chirality : 0.038 0.377 28537 Planarity : 0.006 0.129 12110 Dihedral : 15.262 179.947 58656 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.74 % Rotamer: Outliers : 2.97 % Allowed : 15.17 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.63 (0.11), residues: 5527 helix: 1.71 (0.12), residues: 1884 sheet: 0.53 (0.15), residues: 1102 loop : -0.60 (0.12), residues: 2541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 995 time to evaluate : 5.714 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 outliers start: 136 outliers final: 72 residues processed: 1040 average time/residue: 2.2488 time to fit residues: 3270.5699 Evaluate side-chains 1050 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 978 time to evaluate : 5.715 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 26 residues processed: 47 average time/residue: 1.2814 time to fit residues: 108.8372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 879 optimal weight: 0.6980 chunk 668 optimal weight: 7.9990 chunk 461 optimal weight: 0.0570 chunk 98 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 597 optimal weight: 6.9990 chunk 892 optimal weight: 10.0000 chunk 945 optimal weight: 5.9990 chunk 466 optimal weight: 0.6980 chunk 846 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 overall best weight: 2.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN C 201 ASN D 153 GLN E 96 ASN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN c 21 ASN c 88 GLN h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN t 3 ASN v 13 ASN v 78 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 149588 Z= 0.301 Angle : 0.711 16.488 223620 Z= 0.370 Chirality : 0.041 0.411 28537 Planarity : 0.006 0.133 12110 Dihedral : 15.336 179.885 58656 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 4.04 % Allowed : 16.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 5527 helix: 1.56 (0.12), residues: 1875 sheet: 0.49 (0.15), residues: 1120 loop : -0.71 (0.11), residues: 2532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 979 time to evaluate : 6.060 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 outliers start: 185 outliers final: 109 residues processed: 1053 average time/residue: 2.2281 time to fit residues: 3291.9047 Evaluate side-chains 1092 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 983 time to evaluate : 5.691 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 43 residues processed: 67 average time/residue: 1.2638 time to fit residues: 151.1151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 787 optimal weight: 4.9990 chunk 536 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 703 optimal weight: 1.9990 chunk 390 optimal weight: 9.9990 chunk 806 optimal weight: 4.9990 chunk 653 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 482 optimal weight: 8.9990 chunk 848 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS E 23 ASN I 58 ASN M 23 ASN M 26 ASN P 37 GLN P 56 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN e 85 ASN h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 107 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN t 3 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 149588 Z= 0.306 Angle : 0.709 16.237 223620 Z= 0.370 Chirality : 0.041 0.410 28537 Planarity : 0.006 0.133 12110 Dihedral : 15.341 179.999 58656 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.44 % Favored : 96.42 % Rotamer: Outliers : 4.17 % Allowed : 17.22 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.38 (0.11), residues: 5527 helix: 1.48 (0.12), residues: 1879 sheet: 0.45 (0.15), residues: 1119 loop : -0.76 (0.11), residues: 2529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 987 time to evaluate : 6.820 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 outliers start: 191 outliers final: 119 residues processed: 1075 average time/residue: 2.2464 time to fit residues: 3383.2077 Evaluate side-chains 1089 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 970 time to evaluate : 5.720 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 60 residues processed: 60 average time/residue: 1.2925 time to fit residues: 137.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 318 optimal weight: 0.5980 chunk 851 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 555 optimal weight: 0.0670 chunk 233 optimal weight: 10.0000 chunk 946 optimal weight: 0.8980 chunk 785 optimal weight: 0.9990 chunk 438 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 313 optimal weight: 0.5980 chunk 496 optimal weight: 8.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS 3 35 GLN C 201 ASN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 55 ASN O 78 GLN P 37 GLN R 61 ASN S 36 ASN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 ASN h 41 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN s 57 HIS t 3 ASN v 32 HIS ** v 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 149588 Z= 0.128 Angle : 0.577 13.481 223620 Z= 0.312 Chirality : 0.034 0.346 28537 Planarity : 0.005 0.121 12110 Dihedral : 14.949 179.908 58656 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.08 % Favored : 96.80 % Rotamer: Outliers : 3.01 % Allowed : 19.31 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.80 (0.11), residues: 5527 helix: 1.88 (0.12), residues: 1885 sheet: 0.63 (0.15), residues: 1125 loop : -0.55 (0.12), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 975 time to evaluate : 5.797 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: 138 outliers final: 83 residues processed: 1057 average time/residue: 2.2287 time to fit residues: 3309.8680 Evaluate side-chains 1035 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 952 time to evaluate : 5.670 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 61 residues processed: 24 average time/residue: 1.1005 time to fit residues: 53.8999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 912 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 539 optimal weight: 8.9990 chunk 691 optimal weight: 4.9990 chunk 535 optimal weight: 20.0000 chunk 796 optimal weight: 30.0000 chunk 528 optimal weight: 7.9990 chunk 942 optimal weight: 0.9980 chunk 589 optimal weight: 5.9990 chunk 574 optimal weight: 20.0000 chunk 435 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN D 153 GLN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN R 61 ASN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN b 122 GLN b 155 ASN b 197 ASN b 205 ASN e 85 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 86 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN o 40 GLN r 52 GLN s 65 HIS t 3 ASN ** v 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 149588 Z= 0.510 Angle : 0.884 17.372 223620 Z= 0.440 Chirality : 0.050 0.503 28537 Planarity : 0.008 0.140 12110 Dihedral : 15.552 179.812 58656 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.80 % Rotamer: Outliers : 4.28 % Allowed : 19.21 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.15 (0.11), residues: 5527 helix: 1.22 (0.12), residues: 1880 sheet: 0.42 (0.15), residues: 1118 loop : -0.88 (0.11), residues: 2529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 977 time to evaluate : 6.317 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: 196 outliers final: 127 residues processed: 1067 average time/residue: 2.2047 time to fit residues: 3310.4183 Evaluate side-chains 1085 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 958 time to evaluate : 5.728 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 127 outliers final: 62 residues processed: 67 average time/residue: 1.3847 time to fit residues: 159.4935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 583 optimal weight: 3.9990 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 0.7980 chunk 283 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 599 optimal weight: 10.0000 chunk 642 optimal weight: 2.9990 chunk 466 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 740 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN R 61 ASN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN c 25 ASN e 85 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 65 HIS t 3 ASN ** v 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 149588 Z= 0.247 Angle : 0.673 15.877 223620 Z= 0.354 Chirality : 0.039 0.388 28537 Planarity : 0.006 0.130 12110 Dihedral : 15.251 179.955 58656 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 3.21 % Allowed : 20.71 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 5527 helix: 1.49 (0.12), residues: 1875 sheet: 0.43 (0.15), residues: 1137 loop : -0.79 (0.12), residues: 2515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 974 time to evaluate : 6.037 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 outliers start: 147 outliers final: 100 residues processed: 1054 average time/residue: 2.2621 time to fit residues: 3355.1769 Evaluate side-chains 1063 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 963 time to evaluate : 5.812 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 64 residues processed: 37 average time/residue: 1.3580 time to fit residues: 92.1039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 857 optimal weight: 0.9980 chunk 903 optimal weight: 0.0980 chunk 823 optimal weight: 8.9990 chunk 878 optimal weight: 5.9990 chunk 902 optimal weight: 1.9990 chunk 528 optimal weight: 7.9990 chunk 382 optimal weight: 0.4980 chunk 689 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 793 optimal weight: 20.0000 chunk 830 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 55 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 ASN g 142 HIS h 41 GLN h 86 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 65 HIS t 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 149588 Z= 0.146 Angle : 0.597 15.107 223620 Z= 0.320 Chirality : 0.035 0.356 28537 Planarity : 0.005 0.123 12110 Dihedral : 14.963 179.774 58656 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 2.49 % Allowed : 21.76 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.67 (0.11), residues: 5527 helix: 1.79 (0.12), residues: 1878 sheet: 0.59 (0.15), residues: 1124 loop : -0.65 (0.12), residues: 2525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 959 time to evaluate : 5.800 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 outliers start: 114 outliers final: 85 residues processed: 1032 average time/residue: 2.2629 time to fit residues: 3286.4380 Evaluate side-chains 1028 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 943 time to evaluate : 5.785 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 62 residues processed: 24 average time/residue: 1.2424 time to fit residues: 57.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 875 optimal weight: 6.9990 chunk 576 optimal weight: 5.9990 chunk 928 optimal weight: 8.9990 chunk 566 optimal weight: 8.9990 chunk 440 optimal weight: 0.0870 chunk 645 optimal weight: 5.9990 chunk 974 optimal weight: 3.9990 chunk 896 optimal weight: 5.9990 chunk 775 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 599 optimal weight: 10.0000 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN D 37 GLN D 153 GLN ** I 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 ASN M 26 ASN O 78 GLN P 37 GLN S 58 ASN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN b 205 ASN e 85 ASN f 87 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 65 HIS t 3 ASN ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 149588 Z= 0.385 Angle : 0.778 16.676 223620 Z= 0.397 Chirality : 0.044 0.452 28537 Planarity : 0.007 0.136 12110 Dihedral : 15.321 179.970 58656 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 2.20 % Allowed : 22.46 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.29 (0.11), residues: 5527 helix: 1.40 (0.12), residues: 1875 sheet: 0.50 (0.15), residues: 1107 loop : -0.85 (0.11), residues: 2545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 958 time to evaluate : 5.875 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 outliers start: 101 outliers final: 83 residues processed: 1023 average time/residue: 2.2281 time to fit residues: 3226.6391 Evaluate side-chains 1025 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 942 time to evaluate : 5.762 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 60 residues processed: 24 average time/residue: 1.0810 time to fit residues: 53.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 475 optimal weight: 10.0000 chunk 616 optimal weight: 4.9990 chunk 826 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 715 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 777 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 797 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 23 ASN ** I 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 ASN M 26 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN b 192 ASN b 197 ASN ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 85 ASN g 142 HIS h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 65 HIS t 3 ASN ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136720 restraints weight = 198261.754| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 0.73 r_work: 0.3286 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 149588 Z= 0.278 Angle : 0.694 15.163 223620 Z= 0.362 Chirality : 0.040 0.397 28537 Planarity : 0.006 0.131 12110 Dihedral : 15.203 179.826 58656 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.18 % Rotamer: Outliers : 2.16 % Allowed : 22.68 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: 0.33 (0.11), residues: 5527 helix: 1.45 (0.12), residues: 1876 sheet: 0.50 (0.15), residues: 1110 loop : -0.84 (0.11), residues: 2541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44061.15 seconds wall clock time: 764 minutes 55.38 seconds (45895.38 seconds total)