Starting phenix.real_space_refine on Tue Mar 12 17:19:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhg_14731/03_2024/7zhg_14731_updated.pdb" } resolution = 2.25 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= 0.009 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 1533 5.49 5 Mg 90 5.21 5 S 102 5.16 5 C 33216 2.51 5 N 11526 2.21 5 O 17805 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 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "P TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "T PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 13": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 64278 Number of models: 1 Model: "" Number of chains: 69 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: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 368 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "4" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 406 Classifications: {'RNA': 19} Modifications used: {'rna3p': 1, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "2" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Unusual residues: {' MG': 85} Classifications: {'undetermined': 85} Link IDs: {None: 84} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1713, 1713 Classifications: {'water': 1713} Link IDs: {None: 1712} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "M" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Q" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "U" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "5" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "4" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35620 SG CYS C 32 53.872 133.129 146.201 1.00 15.27 S ATOM 35641 SG CYS C 35 53.792 136.157 148.572 1.00 22.42 S ATOM 35803 SG CYS C 55 54.749 132.334 149.640 1.00 18.35 S ATOM 35825 SG CYS C 58 51.032 133.036 148.780 1.00 21.01 S ATOM 35479 SG CYS C 14 63.849 122.047 146.978 1.00 10.50 S ATOM 35498 SG CYS C 17 65.006 118.680 148.613 1.00 13.21 S ATOM 35706 SG CYS C 43 66.109 119.411 144.606 1.00 8.57 S ATOM 35728 SG CYS C 46 62.385 118.668 145.465 1.00 9.13 S ATOM 40320 SG CYS F 128 91.160 116.713 161.372 1.00 5.39 S ATOM 40359 SG CYS F 133 94.938 115.719 162.569 1.00 7.20 S ATOM 40376 SG CYS F 135 93.740 119.404 162.435 1.00 7.85 S ATOM 51111 SG CYS P 21 121.575 127.297 80.028 1.00 12.69 S ATOM 51136 SG CYS P 24 122.238 124.665 82.733 1.00 12.52 S ATOM 51278 SG CYS P 42 119.169 126.807 83.345 1.00 9.43 S ATOM 52769 SG CYS R 16 75.518 49.827 193.024 1.00 20.07 S ATOM 52807 SG CYS R 21 77.172 53.155 192.839 1.00 13.82 S ATOM 53295 SG CYS R 77 73.179 53.187 191.673 1.00 18.20 S ATOM 57258 SG CYS W 20 10.747 83.029 150.485 1.00 24.72 S ATOM 57406 SG CYS W 39 12.587 81.067 153.472 1.00 22.50 S ATOM 57427 SG CYS W 42 10.119 79.049 151.402 1.00 26.37 S Time building chain proxies: 25.28, per 1000 atoms: 0.39 Number of scatterers: 64278 At special positions: 0 Unit cell: (204.68, 185.76, 245.96, 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 102 16.00 P 1533 15.00 Mg 90 11.99 O 17805 8.00 N 11526 7.00 C 33216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.94 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " 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=" SG CYS R 77 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 15 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 40 sheets defined 32.8% alpha, 17.6% beta 480 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 26.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.512A 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: 3.546A 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: 4.817A 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: 4.103A 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: 5.041A pdb=" N LYS B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.774A pdb=" N THR B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.568A 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: 3.533A pdb=" N ILE D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.918A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 118 through 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 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 59 through 67 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 152 through 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: 3.543A 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 48 through 53 Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 106 through 119 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 194 through 209 removed outlier: 3.698A pdb=" N THR F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 removed outlier: 3.571A pdb=" N GLU F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.846A pdb=" N LYS G 28 " --> pdb=" O PRO G 24 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.614A pdb=" N PHE G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 97 through 115 Processing helix chain 'H' and resid 119 through 130 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: 3.587A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 20 removed outlier: 3.813A 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 Proline residue: K 48 - end of helix Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.695A pdb=" N SER K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 90 removed outlier: 3.531A 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: 3.550A 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 86 removed outlier: 4.390A 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: 3.716A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 107 removed outlier: 3.693A pdb=" N ALA M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 removed outlier: 3.971A pdb=" N TRP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.562A 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: 3.562A 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: 4.046A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.374A 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: 3.906A 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 43 Processing helix chain 'Q' and resid 47 through 58 Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.525A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 removed outlier: 3.674A pdb=" N GLN Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 139 removed outlier: 3.601A 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 62 Processing helix chain 'T' and resid 13 through 17 Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.829A 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: 3.806A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 4.848A 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: 3.579A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 147 No H-bonds generated for 'chain 'U' and resid 145 through 147' 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: 3.536A pdb=" N PHE Z 7 " --> pdb=" O ILE Z 3 " (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 161 Processing helix chain '0' and resid 5 through 8 Processing helix chain '0' and resid 16 through 35 removed outlier: 3.559A pdb=" N GLN 0 29 " --> pdb=" O ARG 0 25 " (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: 3.883A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 72 removed outlier: 4.664A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 5.224A 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 119 Processing sheet with id= A, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.828A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 12.607A pdb=" N LYS A 82 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N GLY A 193 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 117 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.624A 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 Processing sheet with id= C, first strand: chain 'A' and resid 18 through 23 removed outlier: 3.793A pdb=" N GLY A 34 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 122 through 126 Processing sheet with id= E, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.522A pdb=" N VAL B 114 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 116 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 117 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 138 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 152 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 154 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.942A 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: 3.869A pdb=" N GLU E 175 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS E 167 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.146A 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: 6.792A pdb=" N TYR E 184 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.841A 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: 5.405A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY F 90 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 5.667A 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: 3.980A pdb=" N ILE G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 4.867A 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: 6.695A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.075A 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: 3.632A 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: 6.951A pdb=" N LYS J 44 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU J 57 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE J 46 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL J 55 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR J 48 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 5.437A 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 69 through 76 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: 6.651A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER M 43 " --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR M 26 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER M 21 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 6.279A 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: 3.924A pdb=" N GLU N 56 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN N 76 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL N 54 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 5.552A 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: 17.739A pdb=" N VAL R 33 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 15.193A pdb=" N TYR R 54 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N GLU R 35 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN R 52 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR R 48 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG R 62 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 85 through 87 removed outlier: 3.735A pdb=" N GLU R 107 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU R 87 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 5.932A 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: 4.558A 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: 6.812A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'W' and resid 26 through 30 removed outlier: 4.475A pdb=" N PHE W 15 " --> pdb=" O LEU W 64 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS W 19 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 5.891A 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: 6.809A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.581A 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: 3.614A 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 removed outlier: 3.500A pdb=" N ALA Z 48 " --> pdb=" O GLN Z 83 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Z' and resid 142 through 149 removed outlier: 6.577A pdb=" N MET Z 183 " --> pdb=" O ARG Z 126 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Z 128 " --> pdb=" O ALA Z 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA Z 181 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE Z 130 " --> pdb=" O LYS Z 179 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS Z 179 " --> pdb=" O ILE Z 130 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE Z 132 " --> pdb=" O GLY Z 177 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY Z 177 " --> pdb=" O ILE Z 132 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY Z 134 " --> pdb=" O VAL Z 175 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL Z 175 " --> pdb=" O GLY Z 134 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '3' and resid 51 through 54 986 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1272 hydrogen bonds 2104 hydrogen bond angles 0 basepair planarities 480 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 99.32 Time building geometry restraints manager: 26.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 6177 1.29 - 1.42: 24553 1.42 - 1.55: 32578 1.55 - 1.69: 3074 1.69 - 1.82: 173 Bond restraints: 66555 Sorted by residual: bond pdb=" C4 LHH 21041 " pdb=" C5 LHH 21041 " ideal model delta sigma weight residual 0.030 1.403 -1.373 2.00e-02 2.50e+03 4.71e+03 bond pdb=" C4 LHH 2 250 " pdb=" C5 LHH 2 250 " ideal model delta sigma weight residual 0.030 1.400 -1.370 2.00e-02 2.50e+03 4.70e+03 bond pdb=" N1 LHH 21041 " pdb=" C6 LHH 21041 " ideal model delta sigma weight residual 0.038 1.325 -1.287 2.00e-02 2.50e+03 4.14e+03 bond pdb=" N1 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 0.038 1.321 -1.283 2.00e-02 2.50e+03 4.11e+03 bond pdb=" C5 LHH 21041 " pdb=" C6 LHH 21041 " ideal model delta sigma weight residual 2.238 1.406 0.832 2.00e-02 2.50e+03 1.73e+03 ... (remaining 66550 not shown) Histogram of bond angle deviations from ideal: 90.44 - 99.97: 7 99.97 - 109.50: 21907 109.50 - 119.04: 42396 119.04 - 128.57: 31151 128.57 - 138.10: 1937 Bond angle restraints: 97398 Sorted by residual: angle pdb=" C TYR P 6 " pdb=" CA TYR P 6 " pdb=" CB TYR P 6 " ideal model delta sigma weight residual 111.17 90.44 20.73 1.53e+00 4.27e-01 1.84e+02 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C8 6MZ 21469 " ideal model delta sigma weight residual 91.39 126.54 -35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N ASN P 7 " pdb=" CA ASN P 7 " pdb=" C ASN P 7 " ideal model delta sigma weight residual 113.18 99.97 13.21 1.33e+00 5.65e-01 9.86e+01 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C4 6MZ 21469 " ideal model delta sigma weight residual 154.15 125.58 28.57 3.00e+00 1.11e-01 9.07e+01 angle pdb=" N LYS X 37 " pdb=" CA LYS X 37 " pdb=" C LYS X 37 " ideal model delta sigma weight residual 110.10 98.53 11.57 1.49e+00 4.50e-01 6.03e+01 ... (remaining 97393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 38501 35.00 - 70.00: 3583 70.00 - 105.00: 505 105.00 - 140.00: 7 140.00 - 175.00: 4 Dihedral angle restraints: 42600 sinusoidal: 32270 harmonic: 10330 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 44.12 155.88 1 1.50e+01 4.44e-03 8.16e+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 66.67 133.33 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" C TYR P 6 " pdb=" N TYR P 6 " pdb=" CA TYR P 6 " pdb=" CB TYR P 6 " ideal model delta harmonic sigma weight residual -122.60 -101.50 -21.10 0 2.50e+00 1.60e-01 7.12e+01 ... (remaining 42597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 11233 0.107 - 0.214: 378 0.214 - 0.321: 10 0.321 - 0.428: 5 0.428 - 0.535: 1 Chirality restraints: 11627 Sorted by residual: chirality pdb=" C3' G 21424 " pdb=" C4' G 21424 " pdb=" O3' G 21424 " pdb=" C2' G 21424 " both_signs ideal model delta sigma weight residual False -2.48 -1.94 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA THR 3 39 " pdb=" N THR 3 39 " pdb=" C THR 3 39 " pdb=" CB THR 3 39 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.80e+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 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 11624 not shown) Planarity restraints: 6691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' MA6 21488 " 0.066 2.00e-02 2.50e+03 6.23e-01 8.73e+03 pdb=" C4' MA6 21488 " 0.463 2.00e-02 2.50e+03 pdb=" O4' MA6 21488 " 0.724 2.00e-02 2.50e+03 pdb=" C3' MA6 21488 " -0.585 2.00e-02 2.50e+03 pdb=" O3' MA6 21488 " -0.646 2.00e-02 2.50e+03 pdb=" C2' MA6 21488 " -0.188 2.00e-02 2.50e+03 pdb=" O2' MA6 21488 " 0.961 2.00e-02 2.50e+03 pdb=" C1' MA6 21488 " 0.201 2.00e-02 2.50e+03 pdb=" N9 MA6 21488 " -0.996 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 934 " 0.083 2.00e-02 2.50e+03 6.16e-01 8.53e+03 pdb=" C4' OMG 2 934 " 0.425 2.00e-02 2.50e+03 pdb=" O4' OMG 2 934 " 0.582 2.00e-02 2.50e+03 pdb=" C3' OMG 2 934 " -0.603 2.00e-02 2.50e+03 pdb=" O3' OMG 2 934 " -0.693 2.00e-02 2.50e+03 pdb=" C2' OMG 2 934 " -0.134 2.00e-02 2.50e+03 pdb=" O2' OMG 2 934 " 1.047 2.00e-02 2.50e+03 pdb=" C1' OMG 2 934 " 0.228 2.00e-02 2.50e+03 pdb=" N9 OMG 2 934 " -0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 846 " 0.071 2.00e-02 2.50e+03 6.13e-01 8.46e+03 pdb=" C4' OMC 2 846 " 0.439 2.00e-02 2.50e+03 pdb=" O4' OMC 2 846 " 0.626 2.00e-02 2.50e+03 pdb=" C3' OMC 2 846 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMC 2 846 " -0.674 2.00e-02 2.50e+03 pdb=" C2' OMC 2 846 " -0.162 2.00e-02 2.50e+03 pdb=" O2' OMC 2 846 " 1.020 2.00e-02 2.50e+03 pdb=" C1' OMC 2 846 " 0.210 2.00e-02 2.50e+03 pdb=" N1 OMC 2 846 " -0.937 2.00e-02 2.50e+03 ... (remaining 6688 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 670 2.49 - 3.09: 41255 3.09 - 3.70: 111453 3.70 - 4.30: 177249 4.30 - 4.90: 243855 Nonbonded interactions: 574482 Sorted by model distance: nonbonded pdb="MG MG 21627 " pdb=" O HOH 23361 " model vdw 1.889 2.170 nonbonded pdb=" OP2 G 2 555 " pdb="MG MG 21624 " model vdw 1.901 2.170 nonbonded pdb="MG MG F 302 " pdb=" O HOH 23382 " model vdw 1.902 2.170 nonbonded pdb="MG MG 21672 " pdb=" O HOH 23036 " model vdw 1.914 2.170 nonbonded pdb=" OP1 C 2 542 " pdb="MG MG 21633 " model vdw 1.919 2.170 ... (remaining 574477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 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: 0.070 Extract box with map and model: 19.000 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 232.760 Find NCS groups from input model: 1.300 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 1.373 66555 Z= 0.929 Angle : 0.854 35.146 97398 Z= 0.426 Chirality : 0.044 0.535 11627 Planarity : 0.058 0.623 6691 Dihedral : 21.527 174.997 35964 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 5.49 % Favored : 93.10 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.63 % 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: 0.18 (0.14), residues: 3545 helix: 1.07 (0.15), residues: 1160 sheet: 0.26 (0.19), residues: 644 loop : -0.53 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 0 16 HIS 0.006 0.001 HIS W 32 PHE 0.032 0.002 PHE I 97 TYR 0.019 0.002 TYR P 27 ARG 0.011 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 643 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8417 (tmt) cc_final: 0.8202 (tmt) REVERT: A 93 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 156 LYS cc_start: 0.8064 (mttt) cc_final: 0.7799 (mppt) REVERT: C 20 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8025 (mt-10) REVERT: G 6 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6466 (tp) REVERT: I 115 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7406 (mt-10) REVERT: K 25 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7437 (mpp-170) REVERT: K 34 GLU cc_start: 0.7844 (mp0) cc_final: 0.7601 (mp0) REVERT: N 99 GLU cc_start: 0.7272 (tt0) cc_final: 0.7049 (tt0) REVERT: T 114 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7617 (mm110) REVERT: U 10 ASP cc_start: 0.7405 (p0) cc_final: 0.7193 (p0) REVERT: U 19 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7295 (tpt-90) REVERT: U 47 GLN cc_start: 0.7370 (mt0) cc_final: 0.6938 (mp-120) REVERT: U 49 ASP cc_start: 0.8110 (p0) cc_final: 0.7870 (p0) outliers start: 43 outliers final: 12 residues processed: 670 average time/residue: 2.0608 time to fit residues: 1682.5604 Evaluate side-chains 500 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 486 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 209 optimal weight: 0.0470 chunk 128 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 236 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 451 optimal weight: 0.4980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN G 118 GLN H 60 ASN K 58 ASN L 21 ASN ** P 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 66555 Z= 0.202 Angle : 1.283 33.766 97398 Z= 0.691 Chirality : 0.041 0.273 11627 Planarity : 0.014 0.142 6691 Dihedral : 23.376 177.177 28327 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.70 % Allowed : 11.27 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3545 helix: 1.54 (0.15), residues: 1162 sheet: 0.51 (0.20), residues: 636 loop : -0.45 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 131 HIS 0.003 0.001 HIS P 41 PHE 0.025 0.001 PHE I 97 TYR 0.014 0.001 TYR P 27 ARG 0.007 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 491 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8279 (tmt) cc_final: 0.8058 (tmt) REVERT: A 93 ILE cc_start: 0.8060 (pt) cc_final: 0.7807 (mm) REVERT: C 20 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8026 (mt-10) REVERT: F 67 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7721 (p0) REVERT: F 115 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7954 (t0) REVERT: H 16 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7084 (pttt) REVERT: I 115 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7363 (mt-10) REVERT: K 25 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7507 (mpp-170) REVERT: L 17 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6666 (tp30) REVERT: L 46 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7005 (ttp-110) REVERT: R 10 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7201 (mm110) REVERT: T 114 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7546 (mm110) REVERT: U 10 ASP cc_start: 0.7356 (p0) cc_final: 0.7146 (p0) REVERT: U 19 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7277 (tpt-90) REVERT: U 47 GLN cc_start: 0.7224 (mt0) cc_final: 0.6859 (mp-120) REVERT: U 49 ASP cc_start: 0.8068 (p0) cc_final: 0.7838 (p0) REVERT: Z 63 ARG cc_start: 0.6036 (mtm180) cc_final: 0.5417 (ttp80) outliers start: 52 outliers final: 22 residues processed: 519 average time/residue: 2.0076 time to fit residues: 1271.9177 Evaluate side-chains 503 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 475 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain W residue 60 ILE Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 250 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 375 optimal weight: 0.0570 chunk 307 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 452 optimal weight: 0.0980 chunk 488 optimal weight: 30.0000 chunk 402 optimal weight: 0.9980 chunk 448 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 362 optimal weight: 0.2980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN H 60 ASN L 21 ASN P 41 HIS R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 66555 Z= 0.207 Angle : 1.230 31.233 97398 Z= 0.670 Chirality : 0.039 0.256 11627 Planarity : 0.013 0.138 6691 Dihedral : 23.337 177.932 28312 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.50 % Allowed : 12.19 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3545 helix: 1.65 (0.15), residues: 1161 sheet: 0.58 (0.20), residues: 631 loop : -0.45 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS P 41 PHE 0.021 0.001 PHE I 97 TYR 0.014 0.001 TYR P 27 ARG 0.007 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 482 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8217 (tmt) cc_final: 0.7644 (ppp) REVERT: A 93 ILE cc_start: 0.8065 (pt) cc_final: 0.7860 (mm) REVERT: B 132 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: C 20 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7970 (mt-10) REVERT: F 67 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7665 (p0) REVERT: G 6 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6473 (tp) REVERT: H 16 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7059 (pttt) REVERT: I 115 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7350 (mt-10) REVERT: K 25 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7495 (mpp-170) REVERT: K 34 GLU cc_start: 0.7812 (mp0) cc_final: 0.7525 (mp0) REVERT: L 17 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6646 (tp30) REVERT: L 46 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6991 (ttp-110) REVERT: R 10 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7182 (mm110) REVERT: T 114 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7562 (mm110) REVERT: U 19 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7281 (tpt-90) REVERT: U 47 GLN cc_start: 0.7242 (mt0) cc_final: 0.6885 (mp-120) REVERT: Z 63 ARG cc_start: 0.5968 (mtm180) cc_final: 0.5466 (ttm110) REVERT: 3 24 GLU cc_start: 0.0747 (mp0) cc_final: 0.0385 (pm20) outliers start: 46 outliers final: 22 residues processed: 507 average time/residue: 1.9800 time to fit residues: 1226.8235 Evaluate side-chains 490 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 461 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain 3 residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 446 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 453 optimal weight: 9.9990 chunk 480 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 430 optimal weight: 0.0770 chunk 129 optimal weight: 20.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN E 139 GLN F 115 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 66555 Z= 0.292 Angle : 1.273 28.609 97398 Z= 0.696 Chirality : 0.044 0.270 11627 Planarity : 0.015 0.147 6691 Dihedral : 23.386 177.706 28307 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.16 % Allowed : 11.96 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3545 helix: 1.53 (0.15), residues: 1173 sheet: 0.47 (0.19), residues: 645 loop : -0.44 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 0 16 HIS 0.006 0.001 HIS W 32 PHE 0.029 0.002 PHE I 97 TYR 0.018 0.002 TYR R 60 ARG 0.010 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 467 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7978 (ttmt) REVERT: F 67 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7813 (p0) REVERT: F 115 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7991 (t0) REVERT: G 6 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6492 (tp) REVERT: H 16 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7128 (pttt) REVERT: I 115 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7427 (mt-10) REVERT: J 82 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: K 25 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7486 (mpp-170) REVERT: L 17 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6635 (tp30) REVERT: L 46 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6922 (mtp180) REVERT: N 40 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.8017 (ttmm) REVERT: R 10 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6737 (mp10) REVERT: T 114 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7618 (mm110) REVERT: U 10 ASP cc_start: 0.7421 (p0) cc_final: 0.7207 (p0) REVERT: U 19 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7295 (tpt-90) REVERT: U 47 GLN cc_start: 0.7270 (mt0) cc_final: 0.6880 (mp-120) REVERT: V 49 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: Z 63 ARG cc_start: 0.6012 (mtm180) cc_final: 0.5498 (ttm110) REVERT: Z 183 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: 3 24 GLU cc_start: 0.0605 (mp0) cc_final: 0.0278 (pm20) outliers start: 66 outliers final: 33 residues processed: 500 average time/residue: 1.9516 time to fit residues: 1196.1344 Evaluate side-chains 507 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 462 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Chi-restraints excluded: chain 3 residue 122 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 400 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 357 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 409 optimal weight: 8.9990 chunk 332 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 431 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN H 60 ASN L 21 ASN R 79 ASN W 25 ASN Z 123 ASN Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 66555 Z= 0.292 Angle : 1.272 28.607 97398 Z= 0.696 Chirality : 0.044 0.270 11627 Planarity : 0.015 0.147 6691 Dihedral : 23.387 177.708 28307 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.54 % Allowed : 12.65 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3545 helix: 1.53 (0.15), residues: 1173 sheet: 0.47 (0.19), residues: 645 loop : -0.44 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 0 16 HIS 0.006 0.001 HIS W 32 PHE 0.029 0.002 PHE I 97 TYR 0.018 0.002 TYR R 60 ARG 0.010 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 462 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7974 (ttmt) REVERT: F 67 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7810 (p0) REVERT: F 115 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7991 (t0) REVERT: G 6 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6492 (tp) REVERT: H 16 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7128 (pttt) REVERT: I 115 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7427 (mt-10) REVERT: J 82 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: K 25 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7487 (mpp-170) REVERT: L 17 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6635 (tp30) REVERT: L 46 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6922 (mtp180) REVERT: N 40 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (ttmm) REVERT: R 10 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6737 (mp10) REVERT: T 114 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7618 (mm110) REVERT: U 10 ASP cc_start: 0.7421 (p0) cc_final: 0.7207 (p0) REVERT: U 19 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7295 (tpt-90) REVERT: U 47 GLN cc_start: 0.7270 (mt0) cc_final: 0.6880 (mp-120) REVERT: V 49 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: Z 63 ARG cc_start: 0.5996 (mtm180) cc_final: 0.5498 (ttm110) REVERT: Z 183 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7629 (ttp) REVERT: Z 186 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6359 (p0) REVERT: 3 24 GLU cc_start: 0.0604 (mp0) cc_final: 0.0279 (pm20) outliers start: 47 outliers final: 33 residues processed: 483 average time/residue: 1.9414 time to fit residues: 1152.4439 Evaluate side-chains 507 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 461 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Chi-restraints excluded: chain 3 residue 122 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 161 optimal weight: 1.9990 chunk 432 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 252 optimal weight: 0.0670 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN E 139 GLN F 115 ASN H 60 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 66555 Z= 0.193 Angle : 1.149 29.356 97398 Z= 0.650 Chirality : 0.040 0.262 11627 Planarity : 0.014 0.141 6691 Dihedral : 23.350 179.990 28307 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.60 % Allowed : 12.91 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % 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: 0.65 (0.14), residues: 3545 helix: 1.65 (0.15), residues: 1169 sheet: 0.57 (0.20), residues: 633 loop : -0.43 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 131 HIS 0.003 0.001 HIS W 32 PHE 0.025 0.001 PHE I 97 TYR 0.019 0.001 TYR F 116 ARG 0.008 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 465 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: F 67 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (p0) REVERT: H 16 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7020 (pttt) REVERT: I 115 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7388 (mt-10) REVERT: J 82 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: K 25 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7466 (mpp-170) REVERT: L 17 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: L 46 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6993 (ttp-110) REVERT: R 10 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7193 (mm110) REVERT: T 114 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7572 (mm110) REVERT: U 19 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7320 (tpt-90) REVERT: U 47 GLN cc_start: 0.7223 (mt0) cc_final: 0.6838 (mp-120) REVERT: Z 23 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7044 (tppt) REVERT: Z 183 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7611 (ttp) REVERT: 3 24 GLU cc_start: 0.0701 (mp0) cc_final: 0.0385 (pm20) outliers start: 49 outliers final: 29 residues processed: 490 average time/residue: 1.9483 time to fit residues: 1171.9880 Evaluate side-chains 492 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 454 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 463 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 479 optimal weight: 0.9990 chunk 299 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN E 139 GLN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 66555 Z= 0.300 Angle : 1.249 26.731 97398 Z= 0.691 Chirality : 0.044 0.274 11627 Planarity : 0.015 0.146 6691 Dihedral : 23.404 178.588 28307 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.80 % Allowed : 12.84 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3545 helix: 1.48 (0.15), residues: 1178 sheet: 0.43 (0.19), residues: 647 loop : -0.46 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 23 HIS 0.006 0.001 HIS W 32 PHE 0.032 0.002 PHE I 97 TYR 0.019 0.002 TYR R 60 ARG 0.012 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 459 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8133 (ttmt) REVERT: F 67 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7805 (p0) REVERT: H 16 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7117 (pttt) REVERT: I 115 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7425 (mt-10) REVERT: J 82 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: K 25 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7481 (mpp-170) REVERT: L 46 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6936 (mtp180) REVERT: R 10 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: T 114 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7614 (mm110) REVERT: U 10 ASP cc_start: 0.7357 (p0) cc_final: 0.7131 (p0) REVERT: U 19 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7299 (tpt-90) REVERT: U 47 GLN cc_start: 0.7296 (mt0) cc_final: 0.6914 (mp-120) REVERT: V 49 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: Z 23 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7126 (tppt) REVERT: Z 183 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: 3 24 GLU cc_start: 0.0782 (mp0) cc_final: 0.0460 (pm20) outliers start: 55 outliers final: 34 residues processed: 487 average time/residue: 1.9781 time to fit residues: 1182.3201 Evaluate side-chains 501 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 458 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 296 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN F 115 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 66555 Z= 0.377 Angle : 1.291 25.603 97398 Z= 0.709 Chirality : 0.047 0.279 11627 Planarity : 0.015 0.148 6691 Dihedral : 23.423 179.364 28307 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.25 % Allowed : 12.42 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % 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: 0.40 (0.14), residues: 3545 helix: 1.34 (0.15), residues: 1177 sheet: 0.43 (0.19), residues: 635 loop : -0.50 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Y 38 HIS 0.007 0.002 HIS W 32 PHE 0.035 0.003 PHE I 97 TYR 0.022 0.002 TYR J 49 ARG 0.011 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 459 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8403 (tmt) cc_final: 0.7914 (ppp) REVERT: D 20 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: F 67 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7837 (p0) REVERT: F 115 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7958 (t0) REVERT: H 16 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7153 (pttt) REVERT: I 115 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7451 (mt-10) REVERT: J 82 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: K 25 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7493 (mpp-170) REVERT: L 46 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6908 (mtp180) REVERT: R 10 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: T 114 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7621 (mm110) REVERT: U 10 ASP cc_start: 0.7378 (p0) cc_final: 0.7163 (p0) REVERT: U 19 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7304 (tpt-90) REVERT: U 47 GLN cc_start: 0.7341 (mt0) cc_final: 0.6958 (mp-120) REVERT: V 49 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: Z 23 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7136 (tppt) REVERT: Z 183 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7727 (ttp) REVERT: 3 24 GLU cc_start: 0.0768 (mp0) cc_final: 0.0428 (pm20) outliers start: 69 outliers final: 42 residues processed: 499 average time/residue: 1.9655 time to fit residues: 1204.5282 Evaluate side-chains 509 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 457 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 2.9990 chunk 458 optimal weight: 0.0270 chunk 418 optimal weight: 7.9990 chunk 446 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 350 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 403 optimal weight: 0.8980 chunk 422 optimal weight: 1.9990 chunk 444 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 66555 Z= 0.212 Angle : 1.181 25.628 97398 Z= 0.665 Chirality : 0.041 0.406 11627 Planarity : 0.014 0.144 6691 Dihedral : 23.379 179.549 28307 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.83 % Allowed : 12.91 % Favored : 85.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3545 helix: 1.47 (0.15), residues: 1176 sheet: 0.45 (0.20), residues: 640 loop : -0.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 0 16 HIS 0.004 0.001 HIS O 120 PHE 0.026 0.002 PHE I 97 TYR 0.017 0.002 TYR P 27 ARG 0.017 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 459 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8339 (tmt) cc_final: 0.7853 (ppp) REVERT: D 20 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: F 67 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7791 (p0) REVERT: H 16 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7070 (pttt) REVERT: I 115 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7403 (mt-10) REVERT: J 82 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: K 25 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7471 (mpp-170) REVERT: L 46 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6986 (mtp180) REVERT: R 10 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: T 114 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7606 (mm110) REVERT: U 10 ASP cc_start: 0.7333 (p0) cc_final: 0.7121 (p0) REVERT: U 19 ARG cc_start: 0.7662 (tpp80) cc_final: 0.7282 (tpt-90) REVERT: U 47 GLN cc_start: 0.7280 (mt0) cc_final: 0.6897 (mp-120) REVERT: V 49 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6476 (mt-10) REVERT: Z 23 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.7100 (ttmt) REVERT: Z 63 ARG cc_start: 0.6011 (mtm180) cc_final: 0.5455 (ttp80) REVERT: Z 67 ARG cc_start: 0.6094 (mmm160) cc_final: 0.5851 (tpm-80) REVERT: Z 183 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: 3 24 GLU cc_start: 0.0798 (mp0) cc_final: 0.0503 (pm20) outliers start: 56 outliers final: 38 residues processed: 490 average time/residue: 1.9660 time to fit residues: 1182.5396 Evaluate side-chains 504 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 457 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 293 optimal weight: 10.0000 chunk 472 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 495 optimal weight: 20.0000 chunk 455 optimal weight: 0.0370 chunk 394 optimal weight: 0.0570 chunk 40 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN F 115 ASN H 60 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 66555 Z= 0.212 Angle : 1.181 25.628 97398 Z= 0.665 Chirality : 0.041 0.405 11627 Planarity : 0.014 0.144 6691 Dihedral : 23.379 179.549 28307 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.60 % Allowed : 13.17 % Favored : 85.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3545 helix: 1.47 (0.15), residues: 1176 sheet: 0.45 (0.20), residues: 640 loop : -0.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 0 16 HIS 0.004 0.001 HIS O 120 PHE 0.026 0.002 PHE I 97 TYR 0.017 0.002 TYR P 27 ARG 0.017 0.000 ARG F 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 457 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8339 (tmt) cc_final: 0.7853 (ppp) REVERT: D 20 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: F 67 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7790 (p0) REVERT: H 16 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7070 (pttt) REVERT: I 115 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7403 (mt-10) REVERT: J 82 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: K 25 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7471 (mpp-170) REVERT: L 46 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6986 (mtp180) REVERT: R 10 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: T 114 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7606 (mm110) REVERT: U 10 ASP cc_start: 0.7333 (p0) cc_final: 0.7121 (p0) REVERT: U 19 ARG cc_start: 0.7662 (tpp80) cc_final: 0.7282 (tpt-90) REVERT: U 47 GLN cc_start: 0.7280 (mt0) cc_final: 0.6897 (mp-120) REVERT: V 49 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6476 (mt-10) REVERT: Z 23 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.7099 (ttmt) REVERT: Z 63 ARG cc_start: 0.6012 (mtm180) cc_final: 0.5455 (ttp80) REVERT: Z 67 ARG cc_start: 0.6094 (mmm160) cc_final: 0.5852 (tpm-80) REVERT: Z 183 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (ttp) REVERT: 3 24 GLU cc_start: 0.0798 (mp0) cc_final: 0.0503 (pm20) outliers start: 49 outliers final: 38 residues processed: 483 average time/residue: 2.0016 time to fit residues: 1187.0845 Evaluate side-chains 504 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 457 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 63 ASP Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 34 MET Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 129 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 10 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain V residue 49 GLU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 159 GLU Chi-restraints excluded: chain Z residue 183 MET Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 63 VAL Chi-restraints excluded: chain 3 residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 313 optimal weight: 6.9990 chunk 420 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 394 optimal weight: 0.0870 chunk 165 optimal weight: 9.9990 chunk 405 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 4.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN F 115 ASN H 60 ASN L 21 ASN R 79 ASN W 25 ASN Z 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.113331 restraints weight = 59262.189| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 0.69 r_work: 0.2985 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 66555 Z= 0.211 Angle : 1.181 25.630 97398 Z= 0.665 Chirality : 0.041 0.401 11627 Planarity : 0.014 0.144 6691 Dihedral : 23.379 179.547 28307 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.60 % Allowed : 13.17 % Favored : 85.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3545 helix: 1.47 (0.15), residues: 1176 sheet: 0.45 (0.20), residues: 640 loop : -0.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 0 16 HIS 0.004 0.001 HIS O 120 PHE 0.026 0.002 PHE I 97 TYR 0.017 0.002 TYR P 27 ARG 0.017 0.000 ARG F 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18871.04 seconds wall clock time: 329 minutes 28.74 seconds (19768.74 seconds total)