Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 10:16:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zah_14580/10_2023/7zah_14580_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 38 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 1599 5.49 5 Mg 63 5.21 5 S 110 5.16 5 C 37314 2.51 5 N 12724 2.21 5 O 17550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 69366 Number of models: 1 Model: "" Number of chains: 58 Chain: "2" Number of atoms: 32312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1497, 32312 Classifications: {'RNA': 1497} Modifications used: {'rna2p': 5, 'rna2p_pur': 114, 'rna2p_pyr': 76, 'rna3p': 62, 'rna3p_pur': 715, 'rna3p_pyr': 524} Link IDs: {'rna2p': 195, 'rna3p': 1301} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Chain: "A" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1531 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 6, 'TRANS': 50} Chain: "D" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1452 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1725 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 123} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 986 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 809 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 137} Chain: "O" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1134 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "Q" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 884 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "S" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 137} Chain: "V" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 808 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "W" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 470 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "X" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "Y" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1541 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "3" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "5" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 18} Chain: "4" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "7" Number of atoms: 4684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4684 Classifications: {'peptide': 595} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 567} Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Unusual residues: {' MG': 57} Classifications: {'undetermined': 57} Link IDs: {None: 56} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 338 Classifications: {'water': 338} Link IDs: {None: 337} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "0" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35620 SG CYS C 32 53.186 130.849 144.640 1.00 56.89 S ATOM 35641 SG CYS C 35 52.815 133.796 146.804 1.00 65.07 S ATOM 35803 SG CYS C 55 53.844 130.094 147.995 1.00 65.21 S ATOM 35825 SG CYS C 58 50.322 130.603 147.172 1.00 71.25 S ATOM 35479 SG CYS C 14 63.306 119.992 145.654 1.00 41.07 S ATOM 35498 SG CYS C 17 64.487 116.958 147.146 1.00 43.81 S ATOM 35706 SG CYS C 43 65.360 117.633 143.510 1.00 39.39 S ATOM 35728 SG CYS C 46 61.957 116.730 144.045 1.00 38.98 S ATOM 40320 SG CYS F 128 90.516 115.332 160.562 1.00 33.31 S ATOM 40359 SG CYS F 133 93.933 114.603 161.947 1.00 38.32 S ATOM 40376 SG CYS F 135 92.789 118.066 161.828 1.00 37.33 S ATOM 51111 SG CYS P 21 122.257 126.196 79.980 1.00 42.57 S ATOM 51136 SG CYS P 24 123.018 123.600 82.354 1.00 43.99 S ATOM 51251 SG CYS P 39 121.392 122.582 79.082 1.00 40.74 S ATOM 51278 SG CYS P 42 119.847 125.458 82.791 1.00 38.67 S ATOM 52769 SG CYS R 16 75.186 48.434 192.638 1.00 69.79 S ATOM 52807 SG CYS R 21 76.841 51.629 192.316 1.00 57.42 S ATOM 53295 SG CYS R 77 73.554 51.161 190.970 1.00 57.26 S ATOM 57258 SG CYS W 20 10.652 79.971 148.477 1.00 86.72 S ATOM 57406 SG CYS W 39 12.616 78.009 151.473 1.00 72.46 S ATOM 57427 SG CYS W 42 10.320 76.339 149.268 1.00 82.09 S Time building chain proxies: 26.47, per 1000 atoms: 0.38 Number of scatterers: 69366 At special positions: 0 Unit cell: (206.4, 183.18, 246.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 110 16.00 P 1599 15.00 Mg 63 11.99 O 17550 8.00 N 12724 7.00 C 37314 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.49 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 39 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 24 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 48 sheets defined 32.8% alpha, 18.0% beta 468 base pairs and 827 stacking pairs defined. Time for finding SS restraints: 24.92 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.834A pdb=" N LEU A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.514A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 152 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.855A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.584A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.831A pdb=" N LYS B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.724A pdb=" N THR B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.756A pdb=" N GLU B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 179 Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 38 through 59 Processing helix chain 'D' and resid 64 through 79 removed outlier: 3.515A pdb=" N ILE D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.964A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 59 through 68 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 152 through 157 removed outlier: 3.637A pdb=" N LYS E 155 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'F' and resid 3 through 14 removed outlier: 3.640A pdb=" N GLU F 7 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 28 Processing helix chain 'F' and resid 34 through 37 removed outlier: 3.597A pdb=" N ILE F 37 " --> pdb=" O ILE F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 106 through 119 removed outlier: 3.527A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 194 through 210 removed outlier: 3.876A pdb=" N THR F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 removed outlier: 3.592A pdb=" N GLU F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.994A pdb=" N LEU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 57 through 60 removed outlier: 3.571A pdb=" N ASN H 60 " --> pdb=" O GLY H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 57 through 60' Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 97 through 115 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 154 through 172 Processing helix chain 'H' and resid 180 through 193 Processing helix chain 'H' and resid 199 through 214 removed outlier: 3.571A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 18 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 86 through 93 Processing helix chain 'I' and resid 113 through 119 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 89 through 92 No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'K' and resid 33 through 35 No H-bonds generated for 'chain 'K' and resid 33 through 35' Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.744A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU K 47 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Proline residue: K 48 - end of helix Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.906A pdb=" N SER K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 90 Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.642A pdb=" N VAL K 108 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 28 Processing helix chain 'L' and resid 79 through 87 removed outlier: 4.155A pdb=" N GLN L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 46 No H-bonds generated for 'chain 'M' and resid 44 through 46' Processing helix chain 'M' and resid 51 through 53 No H-bonds generated for 'chain 'M' and resid 51 through 53' Processing helix chain 'M' and resid 57 through 74 removed outlier: 3.787A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 108 removed outlier: 3.754A pdb=" N ALA M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 removed outlier: 4.156A pdb=" N TRP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 34 Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.754A pdb=" N SER N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 37 through 41' Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 134 through 139 Processing helix chain 'O' and resid 21 through 27 removed outlier: 4.050A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA O 27 " --> pdb=" O TRP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 43 Processing helix chain 'O' and resid 51 through 53 No H-bonds generated for 'chain 'O' and resid 51 through 53' Processing helix chain 'O' and resid 56 through 67 Processing helix chain 'O' and resid 70 through 72 No H-bonds generated for 'chain 'O' and resid 70 through 72' Processing helix chain 'O' and resid 76 through 78 No H-bonds generated for 'chain 'O' and resid 76 through 78' Processing helix chain 'O' and resid 95 through 111 Processing helix chain 'O' and resid 115 through 122 Processing helix chain 'P' and resid 4 through 7 Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'P' and resid 40 through 50 removed outlier: 3.702A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU P 45 " --> pdb=" O HIS P 41 " (cutoff:3.500A) Proline residue: P 48 - end of helix Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 47 through 58 removed outlier: 3.576A pdb=" N GLY Q 51 " --> pdb=" O THR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.698A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 removed outlier: 3.605A pdb=" N GLU Q 110 " --> pdb=" O ARG Q 106 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 139 removed outlier: 3.621A pdb=" N ARG Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY Q 121 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 44 through 63 Processing helix chain 'T' and resid 13 through 17 Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.551A pdb=" N LYS T 26 " --> pdb=" O GLU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 37 Processing helix chain 'T' and resid 42 through 56 Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'T' and resid 103 through 106 Processing helix chain 'U' and resid 4 through 6 No H-bonds generated for 'chain 'U' and resid 4 through 6' Processing helix chain 'U' and resid 9 through 22 removed outlier: 4.026A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 34 Proline residue: U 33 - end of helix No H-bonds generated for 'chain 'U' and resid 30 through 34' Processing helix chain 'U' and resid 50 through 65 Processing helix chain 'U' and resid 70 through 76 Processing helix chain 'U' and resid 96 through 107 Processing helix chain 'U' and resid 123 through 142 removed outlier: 3.627A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 148 Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 48 through 50 No H-bonds generated for 'chain 'V' and resid 48 through 50' Processing helix chain 'V' and resid 75 through 81 Processing helix chain 'V' and resid 84 through 89 Processing helix chain 'Z' and resid 3 through 24 removed outlier: 3.500A pdb=" N LYS Z 13 " --> pdb=" O ARG Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 55 Processing helix chain 'Z' and resid 62 through 71 Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'Z' and resid 92 through 105 Processing helix chain 'Z' and resid 109 through 122 Processing helix chain 'Z' and resid 156 through 160 Processing helix chain '0' and resid 5 through 8 Processing helix chain '0' and resid 16 through 35 removed outlier: 3.543A pdb=" N GLN 0 29 " --> pdb=" O ARG 0 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG 0 30 " --> pdb=" O LEU 0 26 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 20 Processing helix chain '3' and resid 24 through 29 removed outlier: 3.785A pdb=" N ASP 3 28 " --> pdb=" O GLU 3 24 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR 3 29 " --> pdb=" O ILE 3 25 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 24 through 29' Processing helix chain '3' and resid 36 through 44 removed outlier: 3.741A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 3 42 " --> pdb=" O GLU 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 86 through 89 No H-bonds generated for 'chain '3' and resid 86 through 89' Processing helix chain '3' and resid 109 through 121 Processing helix chain '6' and resid 53 through 56 No H-bonds generated for 'chain '6' and resid 53 through 56' Processing helix chain '6' and resid 88 through 97 Processing helix chain '6' and resid 102 through 106 Processing helix chain '7' and resid 20 through 28 removed outlier: 3.686A pdb=" N LEU 7 24 " --> pdb=" O LYS 7 20 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 39 No H-bonds generated for 'chain '7' and resid 37 through 39' Processing helix chain '7' and resid 51 through 57 Processing helix chain '7' and resid 60 through 64 Processing helix chain '7' and resid 86 through 95 Processing helix chain '7' and resid 111 through 122 Processing helix chain '7' and resid 134 through 136 No H-bonds generated for 'chain '7' and resid 134 through 136' Processing helix chain '7' and resid 148 through 154 removed outlier: 4.317A pdb=" N LYS 7 153 " --> pdb=" O LEU 7 149 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS 7 154 " --> pdb=" O MET 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 176 Processing helix chain '7' and resid 207 through 221 removed outlier: 3.672A pdb=" N SER 7 218 " --> pdb=" O ILE 7 214 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN 7 219 " --> pdb=" O ALA 7 215 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG 7 220 " --> pdb=" O GLY 7 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 7 221 " --> pdb=" O LEU 7 217 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 332 through 343 Processing helix chain '7' and resid 365 through 378 removed outlier: 3.794A pdb=" N LYS 7 378 " --> pdb=" O GLU 7 374 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 404 removed outlier: 4.261A pdb=" N GLU 7 404 " --> pdb=" O SER 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 406 through 408 No H-bonds generated for 'chain '7' and resid 406 through 408' Processing helix chain '7' and resid 420 through 429 Processing helix chain '7' and resid 439 through 459 removed outlier: 3.934A pdb=" N ASP 7 445 " --> pdb=" O LYS 7 441 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS 7 458 " --> pdb=" O GLU 7 454 " (cutoff:3.500A) Processing helix chain '7' and resid 461 through 464 No H-bonds generated for 'chain '7' and resid 461 through 464' Processing helix chain '7' and resid 559 through 567 Processing helix chain '7' and resid 575 through 588 Processing helix chain '7' and resid 593 through 597 Processing sheet with id= A, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.747A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 12.540A pdb=" N LYS A 82 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N GLY A 193 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 117 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 102 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.676A pdb=" N ASP A 73 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 18 through 23 removed outlier: 3.806A pdb=" N GLY A 34 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 122 through 126 Processing sheet with id= E, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.607A pdb=" N VAL B 114 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 116 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE B 117 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 138 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 152 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 154 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.952A pdb=" N VAL B 42 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 28 through 31 Processing sheet with id= H, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= I, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= J, first strand: chain 'E' and resid 90 through 93 Processing sheet with id= K, first strand: chain 'E' and resid 122 through 126 removed outlier: 3.746A pdb=" N GLU E 175 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS E 167 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE E 173 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= M, first strand: chain 'E' and resid 230 through 234 removed outlier: 6.688A pdb=" N TYR E 184 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 212 " --> pdb=" O ILE E 202 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 96 through 103 removed outlier: 6.999A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 90 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN F 63 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 145 through 149 Processing sheet with id= P, first strand: chain 'G' and resid 15 through 22 removed outlier: 4.058A pdb=" N ILE G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N MET G 61 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 84 through 88 Processing sheet with id= R, first strand: chain 'H' and resid 134 through 141 Processing sheet with id= S, first strand: chain 'I' and resid 24 through 27 Processing sheet with id= T, first strand: chain 'I' and resid 71 through 74 removed outlier: 6.747A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE I 101 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 72 through 76 removed outlier: 3.749A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG J 79 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.979A pdb=" N LYS J 44 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU J 57 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE J 46 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL J 55 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR J 48 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS J 53 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 4 through 10 Processing sheet with id= X, first strand: chain 'L' and resid 94 through 100 removed outlier: 4.539A pdb=" N LYS L 70 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU L 40 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 43 through 50 Processing sheet with id= Z, first strand: chain 'M' and resid 38 through 43 removed outlier: 6.684A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER M 43 " --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR M 26 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER M 21 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG M 84 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 83 through 87 removed outlier: 3.976A pdb=" N GLU N 56 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN N 76 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL N 54 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL N 126 " --> pdb=" O GLU N 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 7 through 10 Processing sheet with id= AC, first strand: chain 'R' and resid 100 through 102 removed outlier: 17.779A pdb=" N VAL R 33 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 15.164A pdb=" N TYR R 54 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLU R 35 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN R 52 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR R 48 " --> pdb=" O VAL R 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 85 through 87 removed outlier: 3.564A pdb=" N GLU R 107 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU R 87 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL R 105 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 63 through 65 removed outlier: 4.470A pdb=" N ILE T 63 " --> pdb=" O THR T 80 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 79 through 81 Processing sheet with id= AG, first strand: chain 'U' and resid 111 through 114 Processing sheet with id= AH, first strand: chain 'V' and resid 2 through 11 removed outlier: 6.860A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 26 through 30 removed outlier: 4.454A pdb=" N PHE W 15 " --> pdb=" O LEU W 64 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS W 19 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE W 60 " --> pdb=" O LYS W 19 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 54 through 57 removed outlier: 6.667A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLN X 26 " --> pdb=" O ILE X 14 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'X' and resid 16 through 18 removed outlier: 3.650A pdb=" N GLY X 16 " --> pdb=" O GLN X 26 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Z' and resid 33 through 38 Processing sheet with id= AM, first strand: chain 'Z' and resid 142 through 149 removed outlier: 3.872A pdb=" N GLY Z 127 " --> pdb=" O MET Z 183 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '3' and resid 31 through 33 removed outlier: 4.276A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE 3 102 " --> pdb=" O LYS 3 31 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '3' and resid 51 through 54 Processing sheet with id= AP, first strand: chain '6' and resid 67 through 71 removed outlier: 3.919A pdb=" N TYR 6 84 " --> pdb=" O ILE 6 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN 6 70 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE 6 82 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY 6 80 " --> pdb=" O ILE 6 46 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG 6 48 " --> pdb=" O GLY 6 80 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE 6 82 " --> pdb=" O ARG 6 48 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG 6 50 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR 6 84 " --> pdb=" O ARG 6 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN 6 30 " --> pdb=" O ASP 6 38 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG 6 40 " --> pdb=" O VAL 6 28 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL 6 28 " --> pdb=" O ARG 6 40 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 196 through 198 removed outlier: 9.359A pdb=" N VAL 7 197 " --> pdb=" O PHE 7 127 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL 7 129 " --> pdb=" O VAL 7 197 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA 7 99 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA 7 130 " --> pdb=" O ALA 7 99 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU 7 101 " --> pdb=" O ALA 7 130 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN 7 132 " --> pdb=" O LEU 7 101 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL 7 103 " --> pdb=" O ASN 7 132 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '7' and resid 274 through 278 removed outlier: 3.560A pdb=" N THR 7 277 " --> pdb=" O ILE 7 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY 7 269 " --> pdb=" O PRO 7 325 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR 7 237 " --> pdb=" O ILE 7 255 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE 7 255 " --> pdb=" O THR 7 237 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '7' and resid 240 through 244 removed outlier: 3.600A pdb=" N GLU 7 240 " --> pdb=" O ASP 7 252 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY 7 248 " --> pdb=" O GLU 7 244 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '7' and resid 259 through 261 Processing sheet with id= AU, first strand: chain '7' and resid 433 through 436 removed outlier: 6.585A pdb=" N ILE 7 411 " --> pdb=" O PHE 7 434 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY 7 436 " --> pdb=" O ILE 7 411 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY 7 413 " --> pdb=" O GLY 7 436 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE 7 359 " --> pdb=" O LEU 7 412 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE 7 414 " --> pdb=" O ILE 7 359 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS 7 361 " --> pdb=" O PHE 7 414 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL 7 360 " --> pdb=" O ARG 7 383 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA 7 385 " --> pdb=" O VAL 7 360 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA 7 362 " --> pdb=" O ALA 7 385 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL 7 387 " --> pdb=" O ALA 7 362 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '7' and resid 552 through 554 removed outlier: 6.654A pdb=" N ARG 7 472 " --> pdb=" O VAL 7 493 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL 7 493 " --> pdb=" O ARG 7 472 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1245 hydrogen bonds 2094 hydrogen bond angles 0 basepair planarities 468 basepair parallelities 827 stacking parallelities Total time for adding SS restraints: 55.00 Time building geometry restraints manager: 27.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 7175 1.28 - 1.41: 24185 1.41 - 1.55: 38855 1.55 - 1.68: 3223 1.68 - 1.81: 185 Bond restraints: 73623 Sorted by residual: bond pdb=" C4 LHH 2 250 " pdb=" C5 LHH 2 250 " ideal model delta sigma weight residual 0.030 1.390 -1.360 2.00e-02 2.50e+03 4.63e+03 bond pdb=" C4 LHH 21041 " pdb=" C5 LHH 21041 " ideal model delta sigma weight residual 0.030 1.385 -1.355 2.00e-02 2.50e+03 4.59e+03 bond pdb=" N1 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 0.038 1.310 -1.272 2.00e-02 2.50e+03 4.05e+03 bond pdb=" N1 LHH 21041 " pdb=" C6 LHH 21041 " ideal model delta sigma weight residual 0.038 1.307 -1.269 2.00e-02 2.50e+03 4.03e+03 bond pdb=" C5 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 2.238 1.401 0.837 2.00e-02 2.50e+03 1.75e+03 ... (remaining 73618 not shown) Histogram of bond angle deviations from ideal: 94.39 - 103.05: 3426 103.05 - 111.72: 41199 111.72 - 120.38: 36077 120.38 - 129.04: 24934 129.04 - 137.70: 1627 Bond angle restraints: 107263 Sorted by residual: angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C8 6MZ 21469 " ideal model delta sigma weight residual 91.39 124.14 -32.75 3.00e+00 1.11e-01 1.19e+02 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C4 6MZ 21469 " ideal model delta sigma weight residual 154.15 128.37 25.78 3.00e+00 1.11e-01 7.39e+01 angle pdb=" N6 A2M 2 373 " pdb=" C6 A2M 2 373 " pdb=" N1 A2M 2 373 " ideal model delta sigma weight residual 99.94 120.56 -20.62 3.00e+00 1.11e-01 4.73e+01 angle pdb=" C1' OMG 2 471 " pdb=" N9 OMG 2 471 " pdb=" C4 OMG 2 471 " ideal model delta sigma weight residual 108.29 128.46 -20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" O3' C 4 75 " pdb=" C3' C 4 75 " pdb=" C2' C 4 75 " ideal model delta sigma weight residual 109.50 119.41 -9.91 1.50e+00 4.44e-01 4.37e+01 ... (remaining 107258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 39727 34.78 - 69.55: 1146 69.55 - 104.33: 100 104.33 - 139.10: 8 139.10 - 173.88: 5 Dihedral angle restraints: 40986 sinusoidal: 28687 harmonic: 12299 Sorted by residual: dihedral pdb=" O4' C 2 939 " pdb=" C1' C 2 939 " pdb=" N1 C 2 939 " pdb=" C2 C 2 939 " ideal model delta sinusoidal sigma weight residual 200.00 41.55 158.45 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' C 2 721 " pdb=" C1' C 2 721 " pdb=" N1 C 2 721 " pdb=" C2 C 2 721 " ideal model delta sinusoidal sigma weight residual 200.00 67.97 132.03 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" O4' C 21132 " pdb=" C1' C 21132 " pdb=" N1 C 21132 " pdb=" C2 C 21132 " ideal model delta sinusoidal sigma weight residual 200.00 68.78 131.22 1 1.50e+01 4.44e-03 7.08e+01 ... (remaining 40983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 12683 0.144 - 0.287: 101 0.287 - 0.431: 2 0.431 - 0.574: 0 0.574 - 0.718: 1 Chirality restraints: 12787 Sorted by residual: chirality pdb=" C3' C 4 75 " pdb=" C4' C 4 75 " pdb=" O3' C 4 75 " pdb=" C2' C 4 75 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA SER H 95 " pdb=" N SER H 95 " pdb=" C SER H 95 " pdb=" CB SER H 95 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA LYS 7 355 " pdb=" N LYS 7 355 " pdb=" C LYS 7 355 " pdb=" CB LYS 7 355 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 12784 not shown) Planarity restraints: 7715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 934 " 0.071 2.00e-02 2.50e+03 6.13e-01 8.44e+03 pdb=" C4' OMG 2 934 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMG 2 934 " 0.634 2.00e-02 2.50e+03 pdb=" C3' OMG 2 934 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG 2 934 " -0.667 2.00e-02 2.50e+03 pdb=" C2' OMG 2 934 " -0.164 2.00e-02 2.50e+03 pdb=" O2' OMG 2 934 " 1.006 2.00e-02 2.50e+03 pdb=" C1' OMG 2 934 " 0.216 2.00e-02 2.50e+03 pdb=" N9 OMG 2 934 " -0.941 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 873 " -0.068 2.00e-02 2.50e+03 6.12e-01 8.44e+03 pdb=" C4' OMG 2 873 " -0.444 2.00e-02 2.50e+03 pdb=" O4' OMG 2 873 " -0.695 2.00e-02 2.50e+03 pdb=" C3' OMG 2 873 " 0.603 2.00e-02 2.50e+03 pdb=" O3' OMG 2 873 " 0.629 2.00e-02 2.50e+03 pdb=" C2' OMG 2 873 " 0.192 2.00e-02 2.50e+03 pdb=" O2' OMG 2 873 " -0.971 2.00e-02 2.50e+03 pdb=" C1' OMG 2 873 " -0.202 2.00e-02 2.50e+03 pdb=" N9 OMG 2 873 " 0.955 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 913 " 0.076 2.00e-02 2.50e+03 6.12e-01 8.43e+03 pdb=" C4' OMG 2 913 " 0.434 2.00e-02 2.50e+03 pdb=" O4' OMG 2 913 " 0.594 2.00e-02 2.50e+03 pdb=" C3' OMG 2 913 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG 2 913 " -0.680 2.00e-02 2.50e+03 pdb=" C2' OMG 2 913 " -0.148 2.00e-02 2.50e+03 pdb=" O2' OMG 2 913 " 1.033 2.00e-02 2.50e+03 pdb=" C1' OMG 2 913 " 0.220 2.00e-02 2.50e+03 pdb=" N9 OMG 2 913 " -0.931 2.00e-02 2.50e+03 ... (remaining 7712 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 367 2.11 - 2.80: 17493 2.80 - 3.50: 83031 3.50 - 4.20: 201385 4.20 - 4.90: 290745 Nonbonded interactions: 593021 Sorted by model distance: nonbonded pdb=" O3' A 4 76 " pdb=" C MET 4 101 " model vdw 1.407 3.270 nonbonded pdb=" OE2 GLU N 61 " pdb=" NH2 ARG 6 50 " model vdw 1.445 2.520 nonbonded pdb="MG MG 21624 " pdb=" O HOH 21960 " model vdw 1.764 2.170 nonbonded pdb="MG MG 21633 " pdb=" O HOH 21912 " model vdw 1.768 2.170 nonbonded pdb="MG MG 21624 " pdb=" O HOH 21789 " model vdw 1.776 2.170 ... (remaining 593016 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.050 Extract box with map and model: 18.250 Check model and map are aligned: 0.780 Set scattering table: 0.460 Process input model: 190.710 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 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 : 0.017 1.360 73623 Z= 1.074 Angle : 0.827 32.752 107263 Z= 0.399 Chirality : 0.047 0.718 12787 Planarity : 0.056 0.613 7715 Dihedral : 14.110 173.876 33080 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.24 % Allowed : 5.79 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: -0.04 (0.13), residues: 4228 helix: 0.89 (0.14), residues: 1374 sheet: 0.28 (0.18), residues: 813 loop : -0.74 (0.13), residues: 2041 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 653 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 691 average time/residue: 1.8829 time to fit residues: 1632.2008 Evaluate side-chains 472 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 455 time to evaluate : 3.921 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.6528 time to fit residues: 6.9172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 20.0000 chunk 433 optimal weight: 0.4980 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 448 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 519 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN F 30 GLN G 18 GLN P 41 HIS Q 73 ASN R 71 HIS Z 77 ASN Z 79 GLN Z 83 GLN 0 29 GLN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 73623 Z= 0.255 Angle : 1.282 34.913 107263 Z= 0.677 Chirality : 0.042 0.296 12787 Planarity : 0.014 0.143 7715 Dihedral : 15.025 177.811 24028 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.25 % Allowed : 12.05 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.26 (0.13), residues: 4228 helix: 1.28 (0.14), residues: 1365 sheet: 0.41 (0.18), residues: 805 loop : -0.64 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 483 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 37 residues processed: 529 average time/residue: 1.6767 time to fit residues: 1143.3669 Evaluate side-chains 498 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 461 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 11 average time/residue: 0.7912 time to fit residues: 18.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 432 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 520 optimal weight: 8.9990 chunk 562 optimal weight: 0.8980 chunk 463 optimal weight: 10.0000 chunk 516 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 417 optimal weight: 9.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN F 30 GLN G 18 GLN J 40 GLN L 84 GLN O 67 GLN P 41 HIS Q 73 ASN Z 77 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 73623 Z= 0.324 Angle : 1.245 33.794 107263 Z= 0.669 Chirality : 0.043 0.315 12787 Planarity : 0.014 0.144 7715 Dihedral : 15.043 177.596 24028 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.87 % Allowed : 13.37 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4228 helix: 1.25 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 462 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 46 residues processed: 500 average time/residue: 1.7314 time to fit residues: 1109.1834 Evaluate side-chains 507 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 461 time to evaluate : 3.959 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 32 residues processed: 16 average time/residue: 0.7957 time to fit residues: 25.1117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 7.9990 chunk 391 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 349 optimal weight: 0.7980 chunk 522 optimal weight: 10.0000 chunk 552 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 494 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN J 88 GLN L 84 GLN Q 73 ASN R 79 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 73623 Z= 0.324 Angle : 1.245 33.794 107263 Z= 0.669 Chirality : 0.043 0.315 12787 Planarity : 0.014 0.144 7715 Dihedral : 15.043 177.596 24028 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.91 % Allowed : 14.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4228 helix: 1.25 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 461 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 33 residues processed: 491 average time/residue: 1.7342 time to fit residues: 1090.2832 Evaluate side-chains 483 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 450 time to evaluate : 3.915 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 3 average time/residue: 1.0214 time to fit residues: 9.1815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 411 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 471 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 496 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN J 88 GLN L 84 GLN Q 73 ASN R 79 ASN Z 77 ASN Z 79 GLN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 73623 Z= 0.368 Angle : 1.242 33.466 107263 Z= 0.668 Chirality : 0.044 0.597 12787 Planarity : 0.014 0.145 7715 Dihedral : 15.033 178.322 24028 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.65 % Allowed : 14.47 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.23 (0.12), residues: 4228 helix: 1.23 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 448 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 40 residues processed: 484 average time/residue: 1.7670 time to fit residues: 1097.9033 Evaluate side-chains 487 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 447 time to evaluate : 3.881 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 10 average time/residue: 1.0425 time to fit residues: 19.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 5.9990 chunk 497 optimal weight: 40.0000 chunk 109 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 553 optimal weight: 20.0000 chunk 459 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 290 optimal weight: 0.6980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 HIS F 30 GLN G 18 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN L 84 GLN Q 73 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 73623 Z= 0.368 Angle : 1.242 33.466 107263 Z= 0.668 Chirality : 0.044 0.597 12787 Planarity : 0.014 0.145 7715 Dihedral : 15.033 178.322 24028 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.91 % Allowed : 15.10 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.23 (0.12), residues: 4228 helix: 1.23 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 447 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 33 residues processed: 477 average time/residue: 1.7347 time to fit residues: 1066.5986 Evaluate side-chains 479 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 446 time to evaluate : 4.006 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 3 average time/residue: 1.0534 time to fit residues: 9.4610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 chunk 465 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 chunk 551 optimal weight: 20.0000 chunk 345 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN L 84 GLN Q 73 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 73623 Z= 0.368 Angle : 1.242 33.466 107263 Z= 0.668 Chirality : 0.044 0.597 12787 Planarity : 0.014 0.145 7715 Dihedral : 15.033 178.322 24028 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.88 % Allowed : 15.15 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.23 (0.12), residues: 4228 helix: 1.23 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 32 residues processed: 476 average time/residue: 1.7457 time to fit residues: 1068.7414 Evaluate side-chains 477 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 445 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 2 average time/residue: 0.5896 time to fit residues: 6.8441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 350 optimal weight: 7.9990 chunk 375 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 433 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN L 84 GLN Q 73 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 73623 Z= 0.368 Angle : 1.241 33.464 107263 Z= 0.668 Chirality : 0.044 0.594 12787 Planarity : 0.014 0.145 7715 Dihedral : 15.033 178.319 24028 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.91 % Allowed : 15.12 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.23 (0.12), residues: 4228 helix: 1.23 (0.14), residues: 1372 sheet: 0.39 (0.18), residues: 808 loop : -0.64 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 445 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 33 residues processed: 475 average time/residue: 1.7192 time to fit residues: 1050.9063 Evaluate side-chains 478 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 445 time to evaluate : 3.940 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 3 average time/residue: 1.0007 time to fit residues: 9.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 9.9990 chunk 528 optimal weight: 30.0000 chunk 481 optimal weight: 0.3980 chunk 513 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 403 optimal weight: 0.0770 chunk 157 optimal weight: 0.8980 chunk 464 optimal weight: 8.9990 chunk 485 optimal weight: 9.9990 chunk 511 optimal weight: 8.9990 overall best weight: 2.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 GLN L 84 GLN Q 73 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.247 73623 Z= 0.363 Angle : 1.242 33.452 107263 Z= 0.668 Chirality : 0.044 0.577 12787 Planarity : 0.014 0.144 7715 Dihedral : 15.032 178.302 24028 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.93 % Allowed : 15.10 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % 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: 0.23 (0.12), residues: 4228 helix: 1.23 (0.14), residues: 1372 sheet: 0.40 (0.18), residues: 807 loop : -0.65 (0.13), residues: 2049 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 445 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 33 residues processed: 475 average time/residue: 1.7856 time to fit residues: 1089.3931 Evaluate side-chains 478 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 445 time to evaluate : 4.047 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 3 average time/residue: 1.2686 time to fit residues: 10.2863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 0.4980 chunk 543 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 257 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 569 optimal weight: 10.0000 chunk 524 optimal weight: 1.9990 chunk 453 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 350 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 GLN G 18 GLN J 40 GLN P 41 HIS Q 73 ASN ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 340 GLN 7 510 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 73623 Z= 0.237 Angle : 1.210 32.225 107263 Z= 0.657 Chirality : 0.041 0.393 12787 Planarity : 0.013 0.141 7715 Dihedral : 15.034 179.185 24028 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.10 % Allowed : 14.93 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 4228 helix: 1.34 (0.14), residues: 1366 sheet: 0.42 (0.18), residues: 800 loop : -0.61 (0.13), residues: 2062 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8456 Ramachandran restraints generated. 4228 Oldfield, 0 Emsley, 4228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 459 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 36 residues processed: 493 average time/residue: 1.7351 time to fit residues: 1101.3246 Evaluate side-chains 483 residues out of total 3643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 447 time to evaluate : 3.984 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 7 average time/residue: 0.7964 time to fit residues: 13.5979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 7.9990 chunk 483 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 418 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 454 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 466 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: