Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 11:21:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zag_14579/04_2023/7zag_14579_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 1596 5.49 5 Mg 62 5.21 5 S 108 5.16 5 C 34956 2.51 5 N 12100 2.21 5 O 16850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 42": "OE1" <-> "OE2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 62": "NH1" <-> "NH2" Residue "6 ASP 92": "OD1" <-> "OD2" Residue "7 PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 65678 Number of models: 1 Model: "" Number of chains: 57 Chain: "2" Number of atoms: 32312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1497, 32312 Classifications: {'RNA': 1497} Modifications used: {'rna2p': 5, 'rna2p_pur': 114, 'rna2p_pyr': 76, 'rna3p': 62, 'rna3p_pur': 715, 'rna3p_pyr': 524} Link IDs: {'rna2p': 195, 'rna3p': 1301} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Chain: "A" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1531 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 449 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 6, 'TRANS': 50} Chain: "D" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1452 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1725 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 123} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 986 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 809 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 137} Chain: "O" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1134 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "Q" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1257 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 884 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "S" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 137} Chain: "V" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 808 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "W" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 470 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "X" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "Y" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1541 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "3" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 113} Chain: "5" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 18} Chain: "4" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "7" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1029 Classifications: {'peptide': 130} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 124} Chain: "2" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Unusual residues: {' MG': 58} Classifications: {'undetermined': 58} Link IDs: {None: 57} 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: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "2" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 340 Classifications: {'water': 340} Link IDs: {None: 339} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35620 SG CYS C 32 48.107 120.666 147.899 1.00 92.95 S ATOM 35641 SG CYS C 35 47.732 123.521 150.080 1.00 99.17 S ATOM 35803 SG CYS C 55 48.850 119.839 151.248 1.00 97.14 S ATOM 35825 SG CYS C 58 45.463 120.182 150.323 1.00100.15 S ATOM 35479 SG CYS C 14 59.348 110.836 148.256 1.00 82.54 S ATOM 35498 SG CYS C 17 60.904 107.914 149.640 1.00 84.67 S ATOM 35706 SG CYS C 43 61.474 108.607 145.976 1.00 80.83 S ATOM 35728 SG CYS C 46 58.308 107.407 146.713 1.00 80.06 S ATOM 40320 SG CYS F 128 87.712 108.952 161.782 1.00 73.82 S ATOM 40359 SG CYS F 133 91.158 108.347 163.221 1.00 77.57 S ATOM 40376 SG CYS F 135 89.492 111.765 162.952 1.00 76.64 S ATOM 51111 SG CYS P 21 114.398 122.920 80.014 1.00 85.75 S ATOM 51136 SG CYS P 24 115.364 120.405 82.324 1.00 86.71 S ATOM 51278 SG CYS P 42 112.220 121.844 83.073 1.00 82.06 S ATOM 52769 SG CYS R 16 80.300 40.779 194.246 1.00 97.71 S ATOM 52807 SG CYS R 21 81.577 44.145 194.014 1.00 91.59 S ATOM 53295 SG CYS R 77 78.055 43.609 192.734 1.00 91.87 S ATOM 57258 SG CYS W 20 11.098 65.811 153.084 1.00106.56 S ATOM 57406 SG CYS W 39 13.289 63.785 156.178 1.00102.89 S ATOM 57427 SG CYS W 42 11.186 62.347 153.682 1.00106.14 S Time building chain proxies: 27.63, per 1000 atoms: 0.42 Number of scatterers: 65678 At special positions: 0 Unit cell: (195.22, 178.02, 245.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 108 16.00 P 1596 15.00 Mg 62 11.99 O 16850 8.00 N 12100 7.00 C 34956 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: 25.72 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 18 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 41 sheets defined 32.4% alpha, 17.9% beta 469 base pairs and 789 stacking pairs defined. Time for finding SS restraints: 20.17 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.851A 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 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 90 through 95 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: 4.805A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.622A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 74 through 87 removed outlier: 4.824A pdb=" N LYS B 78 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.699A pdb=" N THR B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.734A pdb=" N GLU B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.563A 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: 3.894A 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 166 through 172 removed outlier: 3.588A pdb=" N MET D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 59 through 68 removed outlier: 3.575A pdb=" N GLU E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 34 through 37 Processing helix chain 'F' and resid 47 through 53 Processing helix chain 'F' and resid 55 through 58 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 106 through 119 removed outlier: 3.503A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 194 through 209 removed outlier: 3.887A pdb=" N THR F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.605A pdb=" N LEU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 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 173 removed outlier: 3.584A pdb=" N CYS H 173 " --> pdb=" O ALA H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 193 Processing helix chain 'H' and resid 199 through 214 removed outlier: 3.554A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 20 removed outlier: 3.697A pdb=" N ARG I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 86 through 93 Processing helix chain 'I' and resid 113 through 119 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 89 through 92 No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'K' and resid 33 through 35 No H-bonds generated for 'chain 'K' and resid 33 through 35' Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.633A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Proline residue: K 48 - end of helix Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.688A pdb=" N SER K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 90 Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.620A pdb=" N VAL K 108 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 28 Processing helix chain 'L' and resid 79 through 87 removed outlier: 4.296A pdb=" N GLN L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE L 85 " --> pdb=" O ALA L 81 " (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: 3.645A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 108 removed outlier: 3.635A pdb=" N ALA M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 removed outlier: 4.095A pdb=" N TRP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.757A 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: 3.725A 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: 3.980A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA O 27 " --> pdb=" O TRP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 43 Processing helix chain 'O' and resid 51 through 53 No H-bonds generated for 'chain 'O' and resid 51 through 53' Processing helix chain 'O' and resid 56 through 67 Processing helix chain 'O' and resid 70 through 72 No H-bonds generated for 'chain 'O' and resid 70 through 72' Processing helix chain 'O' and resid 96 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: 3.853A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU P 45 " --> pdb=" O HIS P 41 " (cutoff:3.500A) Proline residue: P 48 - end of helix Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 47 through 57 removed outlier: 3.656A pdb=" N GLY Q 51 " --> pdb=" O THR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.635A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 removed outlier: 3.545A pdb=" N LYS Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS Q 108 " --> pdb=" O ASN Q 104 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 139 removed outlier: 3.513A pdb=" N ARG Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY Q 121 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 44 through 63 Processing helix chain 'T' and resid 13 through 17 Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.745A pdb=" N LYS T 26 " --> pdb=" O GLU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 37 Processing helix chain 'T' and resid 42 through 56 Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'T' and resid 103 through 106 Processing helix chain 'T' and resid 124 through 126 No H-bonds generated for 'chain 'T' and resid 124 through 126' 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: 3.955A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 5.132A 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: 3.656A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU U 142 " --> pdb=" O LYS U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 148 Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 48 through 50 No H-bonds generated for 'chain 'V' and resid 48 through 50' Processing helix chain 'V' and resid 75 through 81 Processing helix chain 'V' and resid 84 through 89 Processing helix chain 'Z' and resid 3 through 24 Processing helix chain 'Z' and resid 51 through 55 Processing helix chain 'Z' and resid 62 through 71 Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'Z' and resid 92 through 105 Processing helix chain 'Z' and resid 109 through 122 Processing helix chain 'Z' and resid 156 through 160 Processing helix chain '0' and resid 5 through 8 Processing helix chain '0' and resid 16 through 35 removed outlier: 3.681A pdb=" N GLN 0 29 " --> pdb=" O ARG 0 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG 0 30 " --> pdb=" O LEU 0 26 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 20 Processing helix chain '3' and resid 24 through 29 removed outlier: 4.000A pdb=" N ASP 3 28 " --> pdb=" O GLU 3 24 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR 3 29 " --> pdb=" O ILE 3 25 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 24 through 29' Processing helix chain '3' and resid 36 through 44 removed outlier: 3.672A pdb=" N LYS 3 41 " --> pdb=" O ASN 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 84 through 89 removed outlier: 4.192A pdb=" N ALA 3 88 " --> pdb=" O LYS 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 109 through 119 Processing helix chain '6' and resid 53 through 56 No H-bonds generated for 'chain '6' and resid 53 through 56' Processing helix chain '6' and resid 88 through 97 Processing helix chain '6' and resid 102 through 106 Processing helix chain '7' and resid 559 through 567 Processing helix chain '7' and resid 575 through 588 Processing helix chain '7' and resid 593 through 597 Processing sheet with id= A, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.608A pdb=" N ASP A 73 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ALA A 79 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 21 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 34 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= B, 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: 6.092A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 12.684A pdb=" N LYS A 82 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 12.404A pdb=" N GLY A 193 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS A 117 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 102 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 122 through 126 removed outlier: 3.530A pdb=" N LYS A 183 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.522A pdb=" N SER B 71 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 114 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 116 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE B 117 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 138 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 152 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE B 154 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 7.020A pdb=" N VAL B 42 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 28 through 31 Processing sheet with id= G, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= H, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= I, first strand: chain 'E' and resid 90 through 93 Processing sheet with id= J, first strand: chain 'E' and resid 122 through 126 removed outlier: 3.852A pdb=" N GLU E 175 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS E 167 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE E 173 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= L, first strand: chain 'E' and resid 230 through 234 removed outlier: 6.649A pdb=" N TYR E 184 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL E 212 " --> pdb=" O ILE E 202 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 96 through 103 removed outlier: 6.943A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY F 90 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN F 63 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 145 through 149 Processing sheet with id= O, first strand: chain 'G' and resid 15 through 22 removed outlier: 3.767A pdb=" N ILE G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET G 61 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 84 through 88 Processing sheet with id= Q, first strand: chain 'H' and resid 134 through 141 Processing sheet with id= R, first strand: chain 'I' and resid 24 through 27 Processing sheet with id= S, first strand: chain 'I' and resid 71 through 74 removed outlier: 6.815A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE I 101 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 72 through 76 removed outlier: 3.504A pdb=" N ARG J 79 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.932A pdb=" N LYS J 44 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU J 57 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE J 46 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL J 55 " --> pdb=" O ILE J 46 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR J 48 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS J 53 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 3 through 10 Processing sheet with id= W, first strand: chain 'L' and resid 94 through 100 removed outlier: 4.611A pdb=" N LYS L 70 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU L 40 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 43 through 50 Processing sheet with id= Y, first strand: chain 'M' and resid 38 through 43 removed outlier: 6.708A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER M 43 " --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR M 26 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER M 21 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG M 84 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 83 through 87 removed outlier: 3.963A pdb=" N GLU N 56 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN N 76 " --> pdb=" O VAL N 54 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL N 54 " --> pdb=" O GLN N 76 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL N 126 " --> pdb=" O GLU N 106 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 7 through 10 Processing sheet with id= AB, first strand: chain 'R' and resid 100 through 102 removed outlier: 17.793A pdb=" N VAL R 33 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 15.129A pdb=" N TYR R 54 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N GLU R 35 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN R 52 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR R 48 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG R 62 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 85 through 87 removed outlier: 3.618A pdb=" N GLU R 107 " --> pdb=" O ARG R 85 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU R 87 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL R 105 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'T' and resid 63 through 65 removed outlier: 4.502A pdb=" N ILE T 63 " --> pdb=" O THR T 80 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'U' and resid 79 through 81 Processing sheet with id= AF, first strand: chain 'U' and resid 111 through 114 Processing sheet with id= AG, first strand: chain 'V' and resid 2 through 11 removed outlier: 6.842A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 6.641A 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: 7.388A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'W' and resid 26 through 30 removed outlier: 6.366A pdb=" N LYS W 19 " --> pdb=" O ILE W 60 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE W 60 " --> pdb=" O LYS W 19 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 54 through 57 removed outlier: 6.700A pdb=" N LYS X 28 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE X 14 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLN X 26 " --> pdb=" O ILE X 14 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 16 through 18 removed outlier: 3.620A pdb=" N GLY X 16 " --> pdb=" O GLN X 26 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 33 through 38 Processing sheet with id= AL, first strand: chain 'Z' and resid 142 through 149 removed outlier: 3.978A pdb=" N GLY Z 127 " --> pdb=" O MET Z 183 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '3' and resid 31 through 33 removed outlier: 4.067A pdb=" N LYS 3 31 " --> pdb=" O ILE 3 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE 3 102 " --> pdb=" O LYS 3 31 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL 3 99 " --> pdb=" O ILE 3 52 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE 3 52 " --> pdb=" O VAL 3 99 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '6' and resid 67 through 71 removed outlier: 3.919A pdb=" N TYR 6 84 " --> pdb=" O ILE 6 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN 6 70 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE 6 82 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY 6 80 " --> pdb=" O ILE 6 46 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG 6 48 " --> pdb=" O GLY 6 80 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE 6 82 " --> pdb=" O ARG 6 48 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG 6 50 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR 6 84 " --> pdb=" O ARG 6 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN 6 30 " --> pdb=" O ASP 6 38 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG 6 40 " --> pdb=" O VAL 6 28 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL 6 28 " --> pdb=" O ARG 6 40 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 552 through 554 removed outlier: 6.655A pdb=" N ARG 7 472 " --> pdb=" O VAL 7 493 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL 7 493 " --> pdb=" O ARG 7 472 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1244 hydrogen bonds 2108 hydrogen bond angles 0 basepair planarities 469 basepair parallelities 789 stacking parallelities Total time for adding SS restraints: 48.11 Time building geometry restraints manager: 27.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6530 1.28 - 1.42: 24517 1.42 - 1.55: 35447 1.55 - 1.68: 3200 1.68 - 1.81: 181 Bond restraints: 69875 Sorted by residual: bond pdb=" C4 LHH 21041 " pdb=" C5 LHH 21041 " ideal model delta sigma weight residual 0.030 1.395 -1.365 2.00e-02 2.50e+03 4.66e+03 bond pdb=" C4 LHH 2 250 " pdb=" C5 LHH 2 250 " ideal model delta sigma weight residual 0.030 1.394 -1.364 2.00e-02 2.50e+03 4.65e+03 bond pdb=" N1 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 0.038 1.312 -1.274 2.00e-02 2.50e+03 4.06e+03 bond pdb=" N1 LHH 21041 " pdb=" C6 LHH 21041 " ideal model delta sigma weight residual 0.038 1.312 -1.274 2.00e-02 2.50e+03 4.06e+03 bond pdb=" C5 LHH 2 250 " pdb=" C6 LHH 2 250 " ideal model delta sigma weight residual 2.238 1.402 0.836 2.00e-02 2.50e+03 1.75e+03 ... (remaining 69870 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.72: 10252 106.72 - 114.35: 43741 114.35 - 121.98: 33706 121.98 - 129.62: 13416 129.62 - 137.25: 1073 Bond angle restraints: 102188 Sorted by residual: angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C8 6MZ 21469 " ideal model delta sigma weight residual 91.39 124.90 -33.51 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C1' 6MZ 21469 " pdb=" N9 6MZ 21469 " pdb=" C4 6MZ 21469 " ideal model delta sigma weight residual 154.15 127.17 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" N6 A2M 2 373 " pdb=" C6 A2M 2 373 " pdb=" N1 A2M 2 373 " ideal model delta sigma weight residual 99.94 120.87 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C1' OMG 2 657 " pdb=" N9 OMG 2 657 " pdb=" C4 OMG 2 657 " ideal model delta sigma weight residual 108.29 128.31 -20.02 3.00e+00 1.11e-01 4.45e+01 angle pdb=" C1' OMG 2 657 " pdb=" N9 OMG 2 657 " pdb=" C8 OMG 2 657 " ideal model delta sigma weight residual 142.82 123.46 19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 102183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 37709 35.46 - 70.91: 870 70.91 - 106.37: 82 106.37 - 141.83: 7 141.83 - 177.29: 4 Dihedral angle restraints: 38672 sinusoidal: 27711 harmonic: 10961 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 43.99 156.01 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 67.22 132.78 1 1.50e+01 4.44e-03 7.16e+01 dihedral pdb=" O4' C 21132 " pdb=" C1' C 21132 " pdb=" N1 C 21132 " pdb=" C2 C 21132 " ideal model delta sinusoidal sigma weight residual 200.00 67.29 132.71 1 1.50e+01 4.44e-03 7.16e+01 ... (remaining 38669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 10338 0.052 - 0.104: 1519 0.104 - 0.156: 309 0.156 - 0.208: 27 0.208 - 0.260: 7 Chirality restraints: 12200 Sorted by residual: chirality pdb=" CA ARG 6 58 " pdb=" N ARG 6 58 " pdb=" C ARG 6 58 " pdb=" CB ARG 6 58 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+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 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1' A 2 529 " pdb=" O4' A 2 529 " pdb=" C2' A 2 529 " pdb=" N9 A 2 529 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 12197 not shown) Planarity restraints: 7069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' MA6 21488 " 0.071 2.00e-02 2.50e+03 6.21e-01 8.66e+03 pdb=" C4' MA6 21488 " 0.460 2.00e-02 2.50e+03 pdb=" O4' MA6 21488 " 0.705 2.00e-02 2.50e+03 pdb=" C3' MA6 21488 " -0.591 2.00e-02 2.50e+03 pdb=" O3' MA6 21488 " -0.652 2.00e-02 2.50e+03 pdb=" C2' MA6 21488 " -0.187 2.00e-02 2.50e+03 pdb=" O2' MA6 21488 " 0.970 2.00e-02 2.50e+03 pdb=" C1' MA6 21488 " 0.202 2.00e-02 2.50e+03 pdb=" N9 MA6 21488 " -0.980 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 873 " -0.069 2.00e-02 2.50e+03 6.13e-01 8.44e+03 pdb=" C4' OMG 2 873 " -0.438 2.00e-02 2.50e+03 pdb=" O4' OMG 2 873 " -0.656 2.00e-02 2.50e+03 pdb=" C3' OMG 2 873 " 0.605 2.00e-02 2.50e+03 pdb=" O3' OMG 2 873 " 0.652 2.00e-02 2.50e+03 pdb=" C2' OMG 2 873 " 0.176 2.00e-02 2.50e+03 pdb=" O2' OMG 2 873 " -1.000 2.00e-02 2.50e+03 pdb=" C1' OMG 2 873 " -0.211 2.00e-02 2.50e+03 pdb=" N9 OMG 2 873 " 0.941 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4AC 2 319 " 0.069 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' 4AC 2 319 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 4AC 2 319 " 0.597 2.00e-02 2.50e+03 pdb=" C3' 4AC 2 319 " -0.601 2.00e-02 2.50e+03 pdb=" O3' 4AC 2 319 " -0.673 2.00e-02 2.50e+03 pdb=" C2' 4AC 2 319 " -0.151 2.00e-02 2.50e+03 pdb=" O2' 4AC 2 319 " 1.021 2.00e-02 2.50e+03 pdb=" C1' 4AC 2 319 " 0.227 2.00e-02 2.50e+03 pdb=" N1 4AC 2 319 " -0.921 2.00e-02 2.50e+03 ... (remaining 7066 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 347 2.11 - 2.81: 16770 2.81 - 3.50: 80728 3.50 - 4.20: 192926 4.20 - 4.90: 276381 Nonbonded interactions: 567152 Sorted by model distance: nonbonded pdb=" O3' A 4 76 " pdb=" C MET 4 101 " model vdw 1.409 3.270 nonbonded pdb=" OE2 GLU N 61 " pdb=" NH2 ARG 6 50 " model vdw 1.585 2.520 nonbonded pdb="MG MG 21628 " pdb=" O HOH 21713 " model vdw 1.837 2.170 nonbonded pdb=" OP1 G 2 916 " pdb="MG MG 21608 " model vdw 1.838 2.170 nonbonded pdb=" OP1 G 2 554 " pdb="MG MG 21635 " model vdw 1.842 2.170 ... (remaining 567147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 20.080 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 176.620 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 1.365 69875 Z= 1.045 Angle : 0.707 33.510 102188 Z= 0.331 Chirality : 0.040 0.260 12200 Planarity : 0.058 0.621 7069 Dihedral : 13.062 177.287 31630 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.94 % 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: 0.45 (0.13), residues: 3763 helix: 1.53 (0.15), residues: 1188 sheet: 0.30 (0.19), residues: 712 loop : -0.47 (0.14), residues: 1863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 643 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 661 average time/residue: 1.7379 time to fit residues: 1443.0419 Evaluate side-chains 511 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 505 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.3739 time to fit residues: 6.2164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 444 optimal weight: 3.9990 chunk 398 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 268 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 412 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 306 optimal weight: 0.0270 chunk 477 optimal weight: 5.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 37 GLN B 108 ASN J 88 GLN K 5 GLN L 2 GLN L 21 ASN L 84 GLN P 41 HIS R 79 ASN S 31 ASN Z 83 GLN 6 75 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.219 69875 Z= 0.239 Angle : 1.300 35.512 102188 Z= 0.689 Chirality : 0.039 0.270 12200 Planarity : 0.014 0.150 7069 Dihedral : 14.789 178.108 23509 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % 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: 3763 helix: 1.70 (0.15), residues: 1201 sheet: 0.42 (0.19), residues: 712 loop : -0.41 (0.14), residues: 1850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 527 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 547 average time/residue: 1.6768 time to fit residues: 1169.8159 Evaluate side-chains 524 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 503 time to evaluate : 3.692 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 8 residues processed: 14 average time/residue: 0.6397 time to fit residues: 19.6148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 265 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 478 optimal weight: 10.0000 chunk 516 optimal weight: 9.9990 chunk 426 optimal weight: 8.9990 chunk 474 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 383 optimal weight: 0.0770 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN J 88 GLN L 2 GLN L 21 ASN L 84 GLN S 18 ASN U 47 GLN Z 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.146 69875 Z= 0.403 Angle : 1.208 32.113 102188 Z= 0.656 Chirality : 0.042 0.285 12200 Planarity : 0.014 0.144 7069 Dihedral : 14.977 179.005 23509 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % 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: 3763 helix: 1.67 (0.15), residues: 1199 sheet: 0.35 (0.19), residues: 720 loop : -0.48 (0.14), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 499 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 523 average time/residue: 1.6760 time to fit residues: 1118.1145 Evaluate side-chains 516 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 490 time to evaluate : 3.692 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 9 residues processed: 17 average time/residue: 0.6117 time to fit residues: 22.3844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 472 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 321 optimal weight: 0.7980 chunk 480 optimal weight: 0.9990 chunk 508 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 455 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 ASN K 5 GLN L 2 GLN L 21 ASN L 84 GLN R 79 ASN S 18 ASN U 47 GLN Z 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 69875 Z= 0.234 Angle : 1.170 31.130 102188 Z= 0.646 Chirality : 0.038 0.227 12200 Planarity : 0.014 0.154 7069 Dihedral : 14.980 179.442 23509 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3763 helix: 1.74 (0.15), residues: 1191 sheet: 0.35 (0.19), residues: 727 loop : -0.43 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 515 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 24 residues processed: 540 average time/residue: 1.6600 time to fit residues: 1148.0984 Evaluate side-chains 525 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 501 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 10 residues processed: 15 average time/residue: 0.9961 time to fit residues: 26.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 423 optimal weight: 7.9990 chunk 288 optimal weight: 0.9990 chunk 7 optimal weight: 30.0000 chunk 378 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 433 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 259 optimal weight: 0.3980 chunk 456 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN E 121 ASN K 5 GLN L 2 GLN L 21 ASN L 84 GLN V 47 ASN Z 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 69875 Z= 0.287 Angle : 1.140 30.744 102188 Z= 0.640 Chirality : 0.040 0.268 12200 Planarity : 0.014 0.222 7069 Dihedral : 14.995 179.946 23509 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.73 (0.15), residues: 1193 sheet: 0.40 (0.19), residues: 723 loop : -0.46 (0.14), residues: 1847 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 499 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 516 average time/residue: 1.6397 time to fit residues: 1083.4774 Evaluate side-chains 520 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 497 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 12 residues processed: 12 average time/residue: 0.6709 time to fit residues: 17.8714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 171 optimal weight: 6.9990 chunk 457 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 508 optimal weight: 9.9990 chunk 422 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 2 GLN L 21 ASN L 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 69875 Z= 0.287 Angle : 1.140 30.744 102188 Z= 0.640 Chirality : 0.040 0.267 12200 Planarity : 0.014 0.222 7069 Dihedral : 14.995 179.946 23509 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.73 (0.15), residues: 1193 sheet: 0.40 (0.19), residues: 723 loop : -0.46 (0.14), residues: 1847 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 497 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 509 average time/residue: 1.7097 time to fit residues: 1109.4701 Evaluate side-chains 509 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 497 time to evaluate : 5.555 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.5170 time to fit residues: 5.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 490 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 371 optimal weight: 8.9990 chunk 287 optimal weight: 4.9990 chunk 428 optimal weight: 0.2980 chunk 284 optimal weight: 0.9990 chunk 506 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 2 GLN L 21 ASN L 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 69875 Z= 0.287 Angle : 1.140 30.744 102188 Z= 0.640 Chirality : 0.040 0.267 12200 Planarity : 0.014 0.222 7069 Dihedral : 14.995 179.946 23509 Min Nonbonded Distance : 1.516 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.73 (0.15), residues: 1193 sheet: 0.40 (0.19), residues: 723 loop : -0.46 (0.14), residues: 1847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 497 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 509 average time/residue: 1.6822 time to fit residues: 1090.8138 Evaluate side-chains 509 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 497 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.5051 time to fit residues: 5.3304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 313 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 322 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 2 GLN L 21 ASN L 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 69875 Z= 0.376 Angle : 1.134 29.744 102188 Z= 0.639 Chirality : 0.041 0.286 12200 Planarity : 0.014 0.173 7069 Dihedral : 15.007 178.488 23509 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3763 helix: 1.68 (0.15), residues: 1195 sheet: 0.39 (0.19), residues: 718 loop : -0.51 (0.14), residues: 1850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 503 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 520 average time/residue: 1.6713 time to fit residues: 1109.4034 Evaluate side-chains 524 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 499 time to evaluate : 3.690 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 14 residues processed: 12 average time/residue: 0.9509 time to fit residues: 21.2338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 461 optimal weight: 2.9990 chunk 485 optimal weight: 50.0000 chunk 443 optimal weight: 3.9990 chunk 472 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 426 optimal weight: 0.4980 chunk 446 optimal weight: 2.9990 chunk 470 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN K 5 GLN L 2 GLN L 21 ASN L 84 GLN U 47 GLN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 69875 Z= 0.276 Angle : 1.113 29.121 102188 Z= 0.633 Chirality : 0.039 0.302 12200 Planarity : 0.014 0.138 7069 Dihedral : 15.049 178.658 23509 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.73 (0.15), residues: 1196 sheet: 0.41 (0.19), residues: 716 loop : -0.48 (0.14), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 500 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 513 average time/residue: 1.6663 time to fit residues: 1094.3315 Evaluate side-chains 515 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 497 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 8 average time/residue: 0.8644 time to fit residues: 15.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 310 optimal weight: 6.9990 chunk 499 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 chunk 347 optimal weight: 7.9990 chunk 524 optimal weight: 10.0000 chunk 482 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN F 115 ASN K 5 GLN L 2 GLN L 21 ASN L 84 GLN R 79 ASN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.162 69875 Z= 0.303 Angle : 1.112 29.045 102188 Z= 0.634 Chirality : 0.039 0.291 12200 Planarity : 0.014 0.138 7069 Dihedral : 15.046 178.519 23509 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.74 (0.15), residues: 1191 sheet: 0.41 (0.19), residues: 716 loop : -0.49 (0.14), residues: 1856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7526 Ramachandran restraints generated. 3763 Oldfield, 0 Emsley, 3763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 496 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 510 average time/residue: 1.6686 time to fit residues: 1091.6082 Evaluate side-chains 508 residues out of total 3250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 492 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.9458 time to fit residues: 11.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 331 optimal weight: 3.9990 chunk 444 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 417 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 429 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN K 5 GLN L 2 GLN L 21 ASN L 84 GLN ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.061231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.037793 restraints weight = 206658.220| |-----------------------------------------------------------------------------| r_work (start): 0.2414 rms_B_bonded: 2.28 r_work: 0.2290 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2195 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9319 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.162 69875 Z= 0.303 Angle : 1.112 29.045 102188 Z= 0.634 Chirality : 0.039 0.291 12200 Planarity : 0.014 0.138 7069 Dihedral : 15.046 178.519 23509 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3763 helix: 1.74 (0.15), residues: 1191 sheet: 0.41 (0.19), residues: 716 loop : -0.49 (0.14), residues: 1856 =============================================================================== Job complete usr+sys time: 18732.53 seconds wall clock time: 327 minutes 7.88 seconds (19627.88 seconds total)