Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 23:37:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zai_14581/08_2023/7zai_14581_updated.pdb" } resolution = 2.6 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 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 1596 5.49 5 Mg 62 5.21 5 S 107 5.16 5 C 34300 2.51 5 N 11912 2.21 5 O 16666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 64649 Number of models: 1 Model: "" Number of chains: 54 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: "2" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Unusual residues: {' MG': 59} Classifications: {'undetermined': 59} Link IDs: {None: 58} 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: "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: "2" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 342 Classifications: {'water': 342} Link IDs: {None: 341} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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 51.724 128.658 147.067 1.00 79.47 S ATOM 35641 SG CYS C 35 51.414 131.508 149.369 1.00 83.98 S ATOM 35803 SG CYS C 55 52.294 127.741 150.438 1.00 83.33 S ATOM 35825 SG CYS C 58 48.884 128.316 149.612 1.00 86.48 S ATOM 35479 SG CYS C 14 62.257 117.957 147.617 1.00 69.67 S ATOM 35498 SG CYS C 17 63.499 114.885 149.049 1.00 71.05 S ATOM 35706 SG CYS C 43 64.311 115.559 145.329 1.00 68.18 S ATOM 35728 SG CYS C 46 60.977 114.604 146.109 1.00 66.42 S ATOM 40320 SG CYS F 128 90.023 113.772 161.680 1.00 61.16 S ATOM 40359 SG CYS F 133 93.570 113.054 163.110 1.00 63.65 S ATOM 40376 SG CYS F 135 92.113 116.424 162.816 1.00 63.28 S ATOM 51111 SG CYS P 21 119.259 125.959 80.370 1.00 71.46 S ATOM 51136 SG CYS P 24 119.982 123.363 82.711 1.00 72.61 S ATOM 51278 SG CYS P 42 116.877 125.018 83.423 1.00 68.28 S ATOM 52769 SG CYS R 16 77.139 46.202 193.723 1.00 84.17 S ATOM 52807 SG CYS R 21 78.578 49.558 193.502 1.00 77.45 S ATOM 53295 SG CYS R 77 75.110 49.325 192.215 1.00 79.39 S ATOM 57258 SG CYS W 20 10.501 76.659 151.506 1.00 95.49 S ATOM 57406 SG CYS W 39 12.599 74.661 154.627 1.00 89.91 S ATOM 57427 SG CYS W 42 10.345 73.160 152.190 1.00 93.79 S Time building chain proxies: 23.53, per 1000 atoms: 0.36 Number of scatterers: 64649 At special positions: 0 Unit cell: (201.24, 183.18, 245.1, 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 107 16.00 P 1596 15.00 Mg 62 11.99 O 16666 8.00 N 11912 7.00 C 34300 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.55 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " 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 17 " 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 F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " 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 R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " 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 : 18 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 42 sheets defined 32.6% alpha, 18.0% beta 477 base pairs and 784 stacking pairs defined. Time for finding SS restraints: 22.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.775A 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: 3.571A 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: 4.803A 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 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.585A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.331A 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: 4.870A pdb=" N LYS B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.812A pdb=" N THR B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.674A pdb=" N GLU B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.755A 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: 3.606A 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: 4.028A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 118 through 127 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 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 removed outlier: 3.557A pdb=" N GLU E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' 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: 3.581A pdb=" N GLU F 7 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 34 through 37 Processing helix chain 'F' and resid 47 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: 3.516A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.693A 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 209 removed outlier: 3.869A pdb=" N THR F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 removed outlier: 3.534A pdb=" N GLU F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 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 34 through 36 No H-bonds generated for 'chain 'H' and resid 34 through 36' Processing helix chain 'H' and resid 57 through 60 removed outlier: 3.555A 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 70 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: 3.554A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 20 removed outlier: 3.658A pdb=" N ARG I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) 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: 3.662A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Proline residue: K 48 - end of helix Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.668A pdb=" N SER K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 90 removed outlier: 3.706A pdb=" N ALA K 75 " --> pdb=" O PHE K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.672A 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: 4.203A 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: 3.695A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 removed outlier: 3.679A pdb=" N ALA M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 removed outlier: 4.128A pdb=" N TRP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 35 Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.695A 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: 4.077A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA O 27 " --> pdb=" O TRP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 42 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 95 through 111 Processing helix chain 'O' and resid 115 through 122 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' 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: 3.760A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 4.042A 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: 3.572A pdb=" N GLY Q 51 " --> pdb=" O THR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.544A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 removed outlier: 3.583A pdb=" N LYS Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 139 removed outlier: 3.514A pdb=" N ARG Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.788A 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 55 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: 3.969A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 34 No H-bonds generated for 'chain 'U' and resid 32 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: 3.644A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 4.267A 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: 3.517A 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: 3.672A pdb=" N GLN 0 29 " --> pdb=" O ARG 0 25 " (cutoff:3.500A) removed outlier: 3.561A 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 27 No H-bonds generated for 'chain '3' and resid 24 through 27' Processing helix chain '3' and resid 36 through 45 removed outlier: 3.625A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 72 removed outlier: 4.505A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU 3 72 " --> pdb=" O PRO 3 68 " (cutoff:3.500A) 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 sheet with id= A, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.824A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N LYS A 82 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N GLY A 193 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 117 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.648A 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: 3.856A 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 removed outlier: 3.587A pdb=" N LYS A 183 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.504A pdb=" N SER B 71 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 114 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 116 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE B 117 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 138 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 152 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.067A 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: 7.018A 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: 3.856A pdb=" N GLU E 175 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS E 167 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.072A 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: 6.656A pdb=" N TYR E 184 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.941A 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: 6.911A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY F 90 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 5.504A 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: 3.844A pdb=" N ILE G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.235A 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: 6.780A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.119A 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: 3.533A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.594A 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: 6.967A pdb=" N LYS J 44 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU J 57 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE J 46 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL J 55 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR J 48 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 5.344A 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: 4.693A pdb=" N LYS L 70 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.572A 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: 6.668A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER M 43 " --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR M 26 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N SER M 21 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 6.243A 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: 3.978A pdb=" N GLU N 56 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN N 76 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL N 54 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 5.685A 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: 17.759A pdb=" N VAL R 33 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N TYR R 54 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N GLU R 35 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN R 52 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 6.473A 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: 3.696A pdb=" N GLU R 107 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU R 87 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 6.002A 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: 4.498A 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: 6.896A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.808A 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: 6.637A pdb=" N LYS W 19 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 5.964A 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: 6.687A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.577A 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: 3.625A 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: 4.006A 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: 4.199A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.668A 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 66 through 69 removed outlier: 6.538A pdb=" N ASP 6 38 " --> pdb=" O GLU 6 29 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA 6 31 " --> pdb=" O TRP 6 36 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TRP 6 36 " --> pdb=" O ALA 6 31 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY 6 80 " --> pdb=" O ARG 6 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 6 82 " --> pdb=" O ARG 6 50 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE 6 68 " --> pdb=" O VAL 6 83 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1263 hydrogen bonds 2118 hydrogen bond angles 0 basepair planarities 477 basepair parallelities 784 stacking parallelities Total time for adding SS restraints: 48.14 Time building geometry restraints manager: 26.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 6358 1.29 - 1.42: 24258 1.42 - 1.55: 34837 1.55 - 1.68: 3199 1.68 - 1.81: 179 Bond restraints: 68831 Sorted by residual: bond pdb=" C4 LHH 21041 " pdb=" C5 LHH 21041 " ideal model delta sigma weight residual 0.030 1.397 -1.367 2.00e-02 2.50e+03 4.67e+03 bond pdb=" C4 LHH 2 250 " pdb=" C5 LHH 2 250 " ideal model delta sigma weight residual 0.030 1.397 -1.367 2.00e-02 2.50e+03 4.67e+03 bond pdb=" N1 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 0.038 1.317 -1.279 2.00e-02 2.50e+03 4.09e+03 bond pdb=" N1 LHH 21041 " pdb=" C6 LHH 21041 " ideal model delta sigma weight residual 0.038 1.317 -1.279 2.00e-02 2.50e+03 4.09e+03 bond pdb=" C5 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 2.238 1.405 0.833 2.00e-02 2.50e+03 1.73e+03 ... (remaining 68826 not shown) Histogram of bond angle deviations from ideal: 44.24 - 64.40: 1 64.40 - 84.56: 0 84.56 - 104.71: 7579 104.71 - 124.87: 86605 124.87 - 145.03: 6598 Bond angle restraints: 100783 Sorted by residual: angle pdb=" O3' C 4 75 " pdb=" P A 4 76 " pdb=" OP1 A 4 76 " ideal model delta sigma weight residual 108.00 44.24 63.76 3.00e+00 1.11e-01 4.52e+02 angle pdb=" O3' C 4 75 " pdb=" P A 4 76 " pdb=" OP2 A 4 76 " ideal model delta sigma weight residual 108.00 145.03 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C8 6MZ 21469 " ideal model delta sigma weight residual 91.39 124.95 -33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C4 6MZ 21469 " ideal model delta sigma weight residual 154.15 126.98 27.17 3.00e+00 1.11e-01 8.20e+01 angle pdb=" N LYS Z 153 " pdb=" CA LYS Z 153 " pdb=" C LYS Z 153 " ideal model delta sigma weight residual 111.36 120.95 -9.59 1.09e+00 8.42e-01 7.74e+01 ... (remaining 100778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 37028 35.52 - 71.05: 891 71.05 - 106.57: 93 106.57 - 142.09: 9 142.09 - 177.62: 5 Dihedral angle restraints: 38026 sinusoidal: 27437 harmonic: 10589 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 41.93 158.07 1 1.50e+01 4.44e-03 8.22e+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 67.94 132.06 1 1.50e+01 4.44e-03 7.13e+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 68.59 131.41 1 1.50e+01 4.44e-03 7.09e+01 ... (remaining 38023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 11222 0.073 - 0.147: 771 0.147 - 0.220: 39 0.220 - 0.294: 5 0.294 - 0.367: 1 Chirality restraints: 12038 Sorted by residual: chirality pdb=" CA LYS Z 153 " pdb=" N LYS Z 153 " pdb=" C LYS Z 153 " pdb=" CB LYS Z 153 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 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 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA THR O 95 " pdb=" N THR O 95 " pdb=" C THR O 95 " pdb=" CB THR O 95 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 12035 not shown) Planarity restraints: 6890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' MA6 21488 " 0.065 2.00e-02 2.50e+03 6.20e-01 8.65e+03 pdb=" C4' MA6 21488 " 0.464 2.00e-02 2.50e+03 pdb=" O4' MA6 21488 " 0.711 2.00e-02 2.50e+03 pdb=" C3' MA6 21488 " -0.586 2.00e-02 2.50e+03 pdb=" O3' MA6 21488 " -0.648 2.00e-02 2.50e+03 pdb=" C2' MA6 21488 " -0.188 2.00e-02 2.50e+03 pdb=" O2' MA6 21488 " 0.963 2.00e-02 2.50e+03 pdb=" C1' MA6 21488 " 0.202 2.00e-02 2.50e+03 pdb=" N9 MA6 21488 " -0.983 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 873 " -0.065 2.00e-02 2.50e+03 6.10e-01 8.37e+03 pdb=" C4' OMG 2 873 " -0.443 2.00e-02 2.50e+03 pdb=" O4' OMG 2 873 " -0.662 2.00e-02 2.50e+03 pdb=" C3' OMG 2 873 " 0.599 2.00e-02 2.50e+03 pdb=" O3' OMG 2 873 " 0.643 2.00e-02 2.50e+03 pdb=" C2' OMG 2 873 " 0.180 2.00e-02 2.50e+03 pdb=" O2' OMG 2 873 " -0.984 2.00e-02 2.50e+03 pdb=" C1' OMG 2 873 " -0.211 2.00e-02 2.50e+03 pdb=" N9 OMG 2 873 " 0.944 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4AC 2 319 " 0.070 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' 4AC 2 319 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 4AC 2 319 " 0.590 2.00e-02 2.50e+03 pdb=" C3' 4AC 2 319 " -0.598 2.00e-02 2.50e+03 pdb=" O3' 4AC 2 319 " -0.670 2.00e-02 2.50e+03 pdb=" C2' 4AC 2 319 " -0.151 2.00e-02 2.50e+03 pdb=" O2' 4AC 2 319 " 1.020 2.00e-02 2.50e+03 pdb=" C1' 4AC 2 319 " 0.228 2.00e-02 2.50e+03 pdb=" N1 4AC 2 319 " -0.920 2.00e-02 2.50e+03 ... (remaining 6887 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 345 2.11 - 2.80: 15983 2.80 - 3.50: 77246 3.50 - 4.20: 192187 4.20 - 4.90: 271763 Nonbonded interactions: 557524 Sorted by model distance: nonbonded pdb=" O3' A 4 76 " pdb=" C MET 4 101 " model vdw 1.408 3.270 nonbonded pdb=" O2' C 4 16 " pdb=" O5' C 4 61 " model vdw 1.566 2.440 nonbonded pdb=" OP2 A 2 474 " pdb="MG MG 21634 " model vdw 1.847 2.170 nonbonded pdb=" OP1 C 21277 " pdb="MG MG 21641 " model vdw 1.852 2.170 nonbonded pdb=" OP1 G 2 554 " pdb="MG MG 21635 " model vdw 1.860 2.170 ... (remaining 557519 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 19.690 Check model and map are aligned: 0.710 Set scattering table: 0.420 Process input model: 172.580 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 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 : 0.016 1.367 68831 Z= 0.919 Angle : 0.737 63.757 100783 Z= 0.336 Chirality : 0.038 0.367 12038 Planarity : 0.058 0.620 6890 Dihedral : 13.283 177.617 31224 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3635 helix: 1.50 (0.15), residues: 1163 sheet: 0.49 (0.19), residues: 677 loop : -0.42 (0.14), residues: 1795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 656 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 670 average time/residue: 1.7487 time to fit residues: 1459.2399 Evaluate side-chains 531 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 526 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 1.2390 time to fit residues: 7.6406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 402 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 465 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN G 110 ASN L 12 ASN L 84 GLN P 41 HIS Q 5 HIS Q 73 ASN R 79 ASN S 30 HIS Z 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 68831 Z= 0.269 Angle : 1.317 35.211 100783 Z= 0.696 Chirality : 0.040 0.301 12038 Planarity : 0.015 0.151 6890 Dihedral : 15.136 179.421 23366 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3635 helix: 1.71 (0.15), residues: 1171 sheet: 0.54 (0.19), residues: 693 loop : -0.44 (0.14), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 543 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 28 residues processed: 572 average time/residue: 1.6261 time to fit residues: 1173.0042 Evaluate side-chains 556 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 528 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 18 average time/residue: 0.9165 time to fit residues: 28.1789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 387 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 504 optimal weight: 6.9990 chunk 415 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 374 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: A 18 GLN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS L 12 ASN L 84 GLN Q 73 ASN R 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 68831 Z= 0.412 Angle : 1.284 34.416 100783 Z= 0.686 Chirality : 0.043 0.290 12038 Planarity : 0.014 0.149 6890 Dihedral : 15.121 179.249 23366 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3635 helix: 1.64 (0.15), residues: 1168 sheet: 0.53 (0.19), residues: 686 loop : -0.49 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 532 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 32 residues processed: 550 average time/residue: 1.6897 time to fit residues: 1172.7440 Evaluate side-chains 561 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 529 time to evaluate : 3.576 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 11 residues processed: 22 average time/residue: 0.7539 time to fit residues: 30.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 4.9990 chunk 350 optimal weight: 0.0980 chunk 242 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 468 optimal weight: 8.9990 chunk 495 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 443 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 GLN Q 73 ASN R 79 ASN ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 68831 Z= 0.411 Angle : 1.282 34.414 100783 Z= 0.686 Chirality : 0.043 0.290 12038 Planarity : 0.014 0.149 6890 Dihedral : 15.121 179.250 23366 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3635 helix: 1.64 (0.15), residues: 1168 sheet: 0.53 (0.19), residues: 686 loop : -0.49 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 530 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 13 residues processed: 540 average time/residue: 1.6939 time to fit residues: 1152.1626 Evaluate side-chains 542 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 529 time to evaluate : 3.691 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 3 average time/residue: 0.6034 time to fit residues: 7.4407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 369 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 423 optimal weight: 6.9990 chunk 342 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 445 optimal weight: 0.0270 chunk 125 optimal weight: 10.0000 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN R 79 ASN ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.083 68831 Z= 0.410 Angle : 1.281 34.410 100783 Z= 0.685 Chirality : 0.043 0.290 12038 Planarity : 0.014 0.149 6890 Dihedral : 15.121 179.252 23366 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3635 helix: 1.64 (0.15), residues: 1168 sheet: 0.53 (0.19), residues: 686 loop : -0.49 (0.14), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 530 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 541 average time/residue: 1.7127 time to fit residues: 1168.1042 Evaluate side-chains 544 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 531 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 3 average time/residue: 0.5785 time to fit residues: 7.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 291 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 496 optimal weight: 9.9990 chunk 412 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN G 110 ASN L 12 ASN L 25 GLN Q 73 ASN R 79 ASN S 30 HIS Z 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.231 68831 Z= 0.312 Angle : 1.208 31.852 100783 Z= 0.659 Chirality : 0.040 0.749 12038 Planarity : 0.015 0.143 6890 Dihedral : 15.227 179.994 23366 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3635 helix: 1.62 (0.15), residues: 1172 sheet: 0.57 (0.20), residues: 677 loop : -0.45 (0.14), residues: 1786 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 534 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 32 residues processed: 555 average time/residue: 1.7021 time to fit residues: 1192.2603 Evaluate side-chains 554 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 522 time to evaluate : 3.612 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 15 residues processed: 20 average time/residue: 0.8064 time to fit residues: 28.8294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 417 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 494 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 ASN Q 73 ASN R 79 ASN S 30 HIS 0 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.229 68831 Z= 0.312 Angle : 1.208 31.851 100783 Z= 0.658 Chirality : 0.040 0.739 12038 Planarity : 0.015 0.143 6890 Dihedral : 15.227 179.994 23366 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3635 helix: 1.62 (0.15), residues: 1172 sheet: 0.57 (0.20), residues: 677 loop : -0.45 (0.14), residues: 1786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 523 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 535 average time/residue: 1.7116 time to fit residues: 1152.8081 Evaluate side-chains 538 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 522 time to evaluate : 3.613 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 4 average time/residue: 0.9047 time to fit residues: 9.6656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 314 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 388 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN L 12 ASN Q 73 ASN R 79 ASN S 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.129 68831 Z= 0.313 Angle : 1.200 31.719 100783 Z= 0.657 Chirality : 0.040 0.344 12038 Planarity : 0.014 0.145 6890 Dihedral : 15.214 179.891 23366 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3635 helix: 1.62 (0.15), residues: 1171 sheet: 0.52 (0.19), residues: 688 loop : -0.46 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 525 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 539 average time/residue: 1.7029 time to fit residues: 1158.9810 Evaluate side-chains 546 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 523 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 11 average time/residue: 0.8105 time to fit residues: 18.2103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 2.9990 chunk 473 optimal weight: 2.9990 chunk 432 optimal weight: 4.9990 chunk 460 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 200 optimal weight: 0.0170 chunk 361 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 459 optimal weight: 7.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN D 123 GLN L 12 ASN Q 73 ASN R 79 ASN S 30 HIS ** T 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.129 68831 Z= 0.313 Angle : 1.200 31.719 100783 Z= 0.657 Chirality : 0.040 0.344 12038 Planarity : 0.014 0.145 6890 Dihedral : 15.214 179.891 23366 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3635 helix: 1.62 (0.15), residues: 1171 sheet: 0.52 (0.19), residues: 688 loop : -0.46 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 524 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 537 average time/residue: 1.7268 time to fit residues: 1170.7449 Evaluate side-chains 536 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 522 time to evaluate : 3.646 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 2 average time/residue: 0.6004 time to fit residues: 6.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 5.9990 chunk 487 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 511 optimal weight: 50.0000 chunk 470 optimal weight: 0.7980 chunk 406 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN D 123 GLN L 12 ASN Q 73 ASN R 79 ASN S 30 HIS Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 68831 Z= 0.313 Angle : 1.199 31.719 100783 Z= 0.657 Chirality : 0.040 0.343 12038 Planarity : 0.014 0.145 6890 Dihedral : 15.214 179.892 23366 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3635 helix: 1.62 (0.15), residues: 1171 sheet: 0.52 (0.19), residues: 688 loop : -0.46 (0.14), residues: 1776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 523 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 536 average time/residue: 1.7148 time to fit residues: 1155.3085 Evaluate side-chains 536 residues out of total 3141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 522 time to evaluate : 3.666 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 2 average time/residue: 0.5759 time to fit residues: 6.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 407 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 418 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN D 123 GLN L 12 ASN Q 73 ASN R 79 ASN S 30 HIS Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.043244 restraints weight = 181354.705| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 1.61 r_work: 0.2385 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9350 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 68831 Z= 0.260 Angle : 1.170 30.838 100783 Z= 0.653 Chirality : 0.039 0.273 12038 Planarity : 0.014 0.203 6890 Dihedral : 15.237 179.926 23366 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3635 helix: 1.64 (0.15), residues: 1163 sheet: 0.53 (0.19), residues: 688 loop : -0.45 (0.14), residues: 1784 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18922.82 seconds wall clock time: 330 minutes 23.35 seconds (19823.35 seconds total)