Starting phenix.real_space_refine on Wed Mar 20 05:32:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y41_33599/03_2024/7y41_33599_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3237 5.49 5 Mg 407 5.21 5 S 58 5.16 5 C 47858 2.51 5 N 18059 2.21 5 O 27433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 129": "OD1" <-> "OD2" Residue "L GLU 18": "OE1" <-> "OE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L ASP 73": "OD1" <-> "OD2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "O ASP 74": "OD1" <-> "OD2" Residue "O GLU 118": "OE1" <-> "OE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 25": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "U PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 36": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 51": "OD1" <-> "OD2" Residue "U PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 77": "OD1" <-> "OD2" Residue "V ASP 104": "OD1" <-> "OD2" Residue "W ASP 30": "OD1" <-> "OD2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "W ASP 173": "OD1" <-> "OD2" Residue "W GLU 175": "OE1" <-> "OE2" Residue "W GLU 191": "OE1" <-> "OE2" Residue "X ASP 15": "OD1" <-> "OD2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 15": "OD1" <-> "OD2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 34": "OD1" <-> "OD2" Residue "c PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 53": "OE1" <-> "OE2" Residue "e GLU 34": "OE1" <-> "OE2" Residue "f ASP 12": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 97056 Number of models: 1 Model: "" Number of chains: 46 Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 301, 'rna2p_pyr': 149, 'rna3p_pur': 1482, 'rna3p_pyr': 1187} Link IDs: {'rna2p': 450, 'rna3p': 2668} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2105 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 19, 'TRANS': 254} Chain breaks: 1 Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 386 Unusual residues: {' MG': 386} Classifications: {'undetermined': 386} Link IDs: {None: 385} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 92823 SG CYS Y 5 82.389 74.485 95.008 1.00116.16 S ATOM 92845 SG CYS Y 8 85.088 71.773 94.740 1.00122.27 S ATOM 93187 SG CYS Y 52 84.748 74.141 92.000 1.00119.21 S ATOM 93206 SG CYS Y 55 82.110 71.758 92.240 1.00121.06 S ATOM 94774 SG CYS c 15 146.677 74.925 60.590 1.00187.97 S ATOM 94796 SG CYS c 18 144.630 72.763 62.952 1.00196.64 S ATOM 95011 SG CYS c 42 148.106 73.468 63.824 1.00174.43 S ATOM 95032 SG CYS c 45 147.544 71.225 60.852 1.00178.53 S ATOM 96064 SG CYS f 11 185.270 159.208 132.817 1.00141.66 S ATOM 96087 SG CYS f 14 184.496 155.977 134.589 1.00144.12 S ATOM 96196 SG CYS f 27 185.101 159.243 136.604 1.00138.30 S ATOM 96406 SG CYS g 16 184.118 129.163 23.679 1.00336.54 S ATOM 96416 SG CYS g 18 187.644 129.885 22.303 1.00334.41 S ATOM 96564 SG CYS g 38 186.917 129.283 26.068 1.00316.48 S ATOM 96585 SG CYS g 41 185.741 132.473 24.206 1.00320.95 S Time building chain proxies: 38.60, per 1000 atoms: 0.40 Number of scatterers: 97056 At special positions: 0 Unit cell: (249.78, 211.14, 224.94, 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 4 29.99 S 58 16.00 P 3237 15.00 Mg 407 11.99 O 27433 8.00 N 18059 7.00 C 47858 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: 46.71 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 52 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 55 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 8 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 5 " pdb=" ZN c 101 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 18 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 15 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 45 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 32 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 41 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 16 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 18 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 38 " Number of angles added : 21 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6396 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 50 sheets defined 31.1% alpha, 22.7% beta 1082 base pairs and 1493 stacking pairs defined. Time for finding SS restraints: 35.45 Creating SS restraints... Processing helix chain '3' and resid 2 through 12 Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.553A pdb=" N ARG C 14 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 198 through 204 removed outlier: 4.324A pdb=" N SER C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 204 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.723A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 63 through 74 Processing helix chain 'D' and resid 88 through 95 removed outlier: 4.140A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 103 through 121 removed outlier: 3.545A pdb=" N ILE E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.830A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.559A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'F' and resid 9 through 17 removed outlier: 3.945A pdb=" N GLN F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 54 through 69 removed outlier: 4.189A pdb=" N ASN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.886A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 44 Processing helix chain 'I' and resid 53 through 62 removed outlier: 3.922A pdb=" N ARG I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 removed outlier: 3.537A pdb=" N GLU I 67 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY I 68 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP I 70 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU I 71 " --> pdb=" O GLY I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 Processing helix chain 'I' and resid 116 through 126 Processing helix chain 'J' and resid 26 through 32 Processing helix chain 'J' and resid 36 through 50 removed outlier: 3.878A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.622A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 58 through 62 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 107 removed outlier: 4.060A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'K' and resid 131 through 136 removed outlier: 4.278A pdb=" N ALA K 134 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.105A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 117 removed outlier: 4.014A pdb=" N VAL L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.914A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 101 Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 110 through 124 removed outlier: 3.617A pdb=" N LYS N 124 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 37 through 57 Proline residue: O 46 - end of helix removed outlier: 3.628A pdb=" N LYS O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 4.140A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 82 removed outlier: 3.540A pdb=" N VAL O 76 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'P' and resid 9 through 27 Processing helix chain 'P' and resid 67 through 73 Processing helix chain 'P' and resid 76 through 94 Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.347A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 3.554A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 100 Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.523A pdb=" N ALA R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.913A pdb=" N ARG R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.606A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'S' and resid 51 through 57 Processing helix chain 'T' and resid 20 through 29 removed outlier: 3.628A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 removed outlier: 3.605A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'U' and resid 6 through 9 Processing helix chain 'U' and resid 17 through 25 Processing helix chain 'U' and resid 38 through 51 Processing helix chain 'W' and resid 20 through 30 Processing helix chain 'W' and resid 51 through 62 Processing helix chain 'W' and resid 158 through 162 removed outlier: 3.692A pdb=" N ILE W 162 " --> pdb=" O ALA W 159 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 58 Processing helix chain 'Z' and resid 6 through 12 removed outlier: 3.832A pdb=" N GLU Z 12 " --> pdb=" O GLY Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 14 through 39 Processing helix chain 'Z' and resid 44 through 67 removed outlier: 4.185A pdb=" N ARG Z 48 " --> pdb=" O ASN Z 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Z 50 " --> pdb=" O ARG Z 46 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 50 removed outlier: 3.516A pdb=" N ARG a 44 " --> pdb=" O ASN a 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'b' and resid 40 through 49 removed outlier: 4.601A pdb=" N LYS b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA b 46 " --> pdb=" O ARG b 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 20 through 27 removed outlier: 3.670A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 41 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.504A pdb=" N SER e 11 " --> pdb=" O HIS e 7 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS e 12 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 64 Processing helix chain 'f' and resid 29 through 32 Processing helix chain 'g' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.474A pdb=" N ILE C 92 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 82 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 6.852A pdb=" N ILE C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 145 through 146 removed outlier: 5.700A pdb=" N VAL C 145 " --> pdb=" O LYS C 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 17 removed outlier: 5.675A pdb=" N LYS D 10 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS D 30 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 191 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS D 181 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL D 112 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.879A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.724A pdb=" N GLY D 122 " --> pdb=" O MET D 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 14 through 20 removed outlier: 8.776A pdb=" N ILE E 124 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP E 6 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA E 126 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS E 125 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.619A pdb=" N ARG F 95 " --> pdb=" O GLU F 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 126 Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 100 Processing sheet with id=AB6, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.641A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR I 23 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY I 108 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 11 through 15 Processing sheet with id=AB8, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.183A pdb=" N VAL K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TRP K 15 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'L' and resid 92 through 93 removed outlier: 6.350A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA L 84 " --> pdb=" O ARG L 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE L 86 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.975A pdb=" N THR Q 57 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG Q 49 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR Q 24 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS Q 82 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS Q 30 " --> pdb=" O ILE Q 80 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE Q 80 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AC5, first strand: chain 'M' and resid 76 through 79 removed outlier: 5.650A pdb=" N GLN M 76 " --> pdb=" O LYS M 111 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU M 113 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL M 78 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL M 110 " --> pdb=" O LYS M 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.370A pdb=" N ILE N 34 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU N 105 " --> pdb=" O TYR N 32 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 40 through 43 removed outlier: 6.414A pdb=" N LEU N 74 " --> pdb=" O GLU N 91 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP N 93 " --> pdb=" O ARG N 72 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG N 72 " --> pdb=" O TRP N 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 33 through 36 removed outlier: 3.843A pdb=" N MET O 110 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 59 through 64 removed outlier: 6.452A pdb=" N LEU P 51 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA P 62 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL P 49 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER P 64 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE P 47 " --> pdb=" O SER P 64 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 12 through 16 removed outlier: 6.709A pdb=" N TYR S 4 " --> pdb=" O VAL S 42 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL S 42 " --> pdb=" O TYR S 4 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE S 6 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 21 through 25 removed outlier: 7.069A pdb=" N TYR S 84 " --> pdb=" O PHE S 78 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE S 78 " --> pdb=" O TYR S 84 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS S 86 " --> pdb=" O HIS S 76 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS S 76 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN S 88 " --> pdb=" O ARG S 74 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG S 74 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS S 90 " --> pdb=" O LYS S 72 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS S 72 " --> pdb=" O HIS S 90 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLN S 92 " --> pdb=" O GLY S 70 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS S 98 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL S 64 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR S 100 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA S 62 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 9 through 17 removed outlier: 6.397A pdb=" N SER T 9 " --> pdb=" O SER T 116 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER T 116 " --> pdb=" O SER T 9 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR T 11 " --> pdb=" O VAL T 114 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL T 114 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS T 13 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 112 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG T 15 " --> pdb=" O ILE T 110 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE T 110 " --> pdb=" O ARG T 15 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS T 109 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA T 83 " --> pdb=" O HIS T 109 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR T 111 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL T 81 " --> pdb=" O THR T 111 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE T 113 " --> pdb=" O ALA T 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 89 through 94 Processing sheet with id=AD6, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.756A pdb=" N ALA U 13 " --> pdb=" O VAL U 32 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AD8, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.905A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL V 73 " --> pdb=" O THR V 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'V' and resid 83 through 88 removed outlier: 3.533A pdb=" N LYS V 103 " --> pdb=" O ALA V 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 9 through 15 removed outlier: 7.629A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ALA W 95 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU W 97 " --> pdb=" O PRO W 34 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL W 36 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL W 99 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS W 94 " --> pdb=" O ASP W 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU W 98 " --> pdb=" O THR W 80 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR W 80 " --> pdb=" O LEU W 98 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN W 9 " --> pdb=" O THR W 68 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP W 70 " --> pdb=" O ASN W 9 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU W 11 " --> pdb=" O ASP W 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 143 through 149 Processing sheet with id=AE4, first strand: chain 'W' and resid 122 through 126 Processing sheet with id=AE5, first strand: chain 'X' and resid 22 through 23 removed outlier: 6.942A pdb=" N LEU X 59 " --> pdb=" O LEU X 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE8, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AE9, first strand: chain 'a' and resid 34 through 38 Processing sheet with id=AF1, first strand: chain 'b' and resid 28 through 32 Processing sheet with id=AF2, first strand: chain 'c' and resid 21 through 26 removed outlier: 6.811A pdb=" N ARG c 21 " --> pdb=" O CYS c 15 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS c 15 " --> pdb=" O ARG c 21 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF4, first strand: chain 'f' and resid 2 through 4 removed outlier: 4.777A pdb=" N VAL f 23 " --> pdb=" O GLN f 36 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 21 through 26 removed outlier: 7.736A pdb=" N ILE g 33 " --> pdb=" O ASP g 11 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR g 13 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL g 35 " --> pdb=" O THR g 13 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN g 15 " --> pdb=" O VAL g 35 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2778 hydrogen bonds 4438 hydrogen bond angles 0 basepair planarities 1082 basepair parallelities 1493 stacking parallelities Total time for adding SS restraints: 145.15 Time building geometry restraints manager: 50.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12843 1.33 - 1.45: 45589 1.45 - 1.57: 40354 1.57 - 1.69: 6473 1.69 - 1.81: 97 Bond restraints: 105356 Sorted by residual: bond pdb=" C HIS K 40 " pdb=" N LYS K 41 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.89e+00 bond pdb=" C GLU E 19 " pdb=" N LEU E 20 " ideal model delta sigma weight residual 1.333 1.297 0.036 1.69e-02 3.50e+03 4.62e+00 bond pdb=" CB PRO W 141 " pdb=" CG PRO W 141 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.47e+00 bond pdb=" CA SER M 28 " pdb=" C SER M 28 " ideal model delta sigma weight residual 1.525 1.507 0.019 1.02e-02 9.61e+03 3.33e+00 bond pdb=" C THR W 111 " pdb=" N VAL W 112 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.26e-02 6.30e+03 3.31e+00 ... (remaining 105351 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.77: 16947 105.77 - 112.84: 62285 112.84 - 119.90: 36462 119.90 - 126.96: 34641 126.96 - 134.02: 8129 Bond angle restraints: 158464 Sorted by residual: angle pdb=" CA PRO W 141 " pdb=" N PRO W 141 " pdb=" CD PRO W 141 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.70e+01 angle pdb=" C ARG M 43 " pdb=" N LYS M 44 " pdb=" CA LYS M 44 " ideal model delta sigma weight residual 121.90 116.47 5.43 1.26e+00 6.30e-01 1.85e+01 angle pdb=" C GLU N 91 " pdb=" N TRP N 92 " pdb=" CA TRP N 92 " ideal model delta sigma weight residual 122.94 117.08 5.86 1.50e+00 4.44e-01 1.53e+01 angle pdb=" N GLY J 53 " pdb=" CA GLY J 53 " pdb=" C GLY J 53 " ideal model delta sigma weight residual 113.18 122.18 -9.00 2.37e+00 1.78e-01 1.44e+01 angle pdb=" C TYR C 6 " pdb=" N LYS C 7 " pdb=" CA LYS C 7 " ideal model delta sigma weight residual 120.68 114.97 5.71 1.52e+00 4.33e-01 1.41e+01 ... (remaining 158459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 58661 35.58 - 71.17: 8104 71.17 - 106.75: 1014 106.75 - 142.34: 25 142.34 - 177.92: 33 Dihedral angle restraints: 67837 sinusoidal: 57880 harmonic: 9957 Sorted by residual: dihedral pdb=" C4' G A1186 " pdb=" C3' G A1186 " pdb=" C2' G A1186 " pdb=" C1' G A1186 " ideal model delta sinusoidal sigma weight residual -35.00 35.31 -70.31 1 8.00e+00 1.56e-02 9.94e+01 dihedral pdb=" C5' G A1186 " pdb=" C4' G A1186 " pdb=" C3' G A1186 " pdb=" O3' G A1186 " ideal model delta sinusoidal sigma weight residual 147.00 78.08 68.92 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" O4' C A2025 " pdb=" C1' C A2025 " pdb=" N1 C A2025 " pdb=" C2 C A2025 " ideal model delta sinusoidal sigma weight residual -160.00 16.18 -176.18 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 67834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 18951 0.065 - 0.130: 1293 0.130 - 0.194: 108 0.194 - 0.259: 12 0.259 - 0.324: 3 Chirality restraints: 20367 Sorted by residual: chirality pdb=" C3' G A1186 " pdb=" C4' G A1186 " pdb=" O3' G A1186 " pdb=" C2' G A1186 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1' A A1098 " pdb=" O4' A A1098 " pdb=" C2' A A1098 " pdb=" N9 A A1098 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1' A A 756 " pdb=" O4' A A 756 " pdb=" C2' A A 756 " pdb=" N9 A A 756 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 20364 not shown) Planarity restraints: 8077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE W 140 " 0.088 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO W 141 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO W 141 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO W 141 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS c 42 " 0.054 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO c 43 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO c 43 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO c 43 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A1098 " 0.042 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 A A1098 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A A1098 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A A1098 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A1098 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A1098 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A1098 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A A1098 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A A1098 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A1098 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A A1098 " -0.005 2.00e-02 2.50e+03 ... (remaining 8074 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 30 1.94 - 2.68: 7290 2.68 - 3.42: 134298 3.42 - 4.16: 333011 4.16 - 4.90: 440665 Nonbonded interactions: 915294 Sorted by model distance: nonbonded pdb="MG MG A4014 " pdb="MG MG A4371 " model vdw 1.204 1.300 nonbonded pdb=" OP2 G A2812 " pdb="MG MG A4078 " model vdw 1.877 2.170 nonbonded pdb=" O3' A A 908 " pdb="MG MG A4086 " model vdw 1.885 2.170 nonbonded pdb=" OP1 C A1079 " pdb="MG MG A4371 " model vdw 1.891 2.170 nonbonded pdb=" O3' A A2001 " pdb="MG MG A4066 " model vdw 1.896 2.170 ... (remaining 915289 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 group one per residue 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 12.810 Check model and map are aligned: 1.090 Set scattering table: 0.670 Process input model: 351.430 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.004 0.106 105356 Z= 0.271 Angle : 0.627 9.004 158464 Z= 0.333 Chirality : 0.035 0.324 20367 Planarity : 0.005 0.128 8077 Dihedral : 24.407 177.920 61441 Min Nonbonded Distance : 1.204 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.39 (0.14), residues: 3463 helix: 0.29 (0.17), residues: 926 sheet: 0.05 (0.18), residues: 742 loop : -0.62 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 93 HIS 0.010 0.002 HIS M 58 PHE 0.035 0.002 PHE Z 34 TYR 0.028 0.002 TYR g 9 ARG 0.013 0.001 ARG W 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1281 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 ASP cc_start: 0.9030 (t0) cc_final: 0.8765 (t0) REVERT: C 54 LYS cc_start: 0.8892 (tmtt) cc_final: 0.8669 (ttmm) REVERT: C 66 ASP cc_start: 0.8462 (t0) cc_final: 0.7744 (t0) REVERT: C 124 ASP cc_start: 0.8468 (t0) cc_final: 0.7615 (t0) REVERT: D 18 ASP cc_start: 0.8022 (t0) cc_final: 0.7367 (t0) REVERT: D 101 LEU cc_start: 0.9260 (mm) cc_final: 0.8888 (mm) REVERT: D 105 ILE cc_start: 0.9589 (pt) cc_final: 0.9337 (pt) REVERT: D 160 VAL cc_start: 0.9419 (t) cc_final: 0.9204 (t) REVERT: D 210 SER cc_start: 0.8872 (t) cc_final: 0.8410 (p) REVERT: E 76 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8564 (mm-40) REVERT: E 106 MET cc_start: 0.8935 (mmm) cc_final: 0.8466 (mmt) REVERT: E 158 ILE cc_start: 0.9253 (mp) cc_final: 0.8031 (mm) REVERT: E 196 PHE cc_start: 0.9229 (m-80) cc_final: 0.8972 (m-80) REVERT: F 29 TYR cc_start: 0.8236 (m-10) cc_final: 0.7564 (m-10) REVERT: F 45 MET cc_start: 0.8472 (mmt) cc_final: 0.8155 (mmt) REVERT: F 58 ASN cc_start: 0.9473 (m-40) cc_final: 0.9204 (m110) REVERT: F 85 LYS cc_start: 0.9690 (mttt) cc_final: 0.9452 (ptpp) REVERT: F 88 GLU cc_start: 0.8727 (tp30) cc_final: 0.8424 (mm-30) REVERT: F 127 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8781 (mmtt) REVERT: F 139 LEU cc_start: 0.9762 (mt) cc_final: 0.9479 (tp) REVERT: F 170 ASP cc_start: 0.7820 (m-30) cc_final: 0.7298 (m-30) REVERT: F 185 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8050 (mmmt) REVERT: G 57 ASP cc_start: 0.8643 (t0) cc_final: 0.8386 (t70) REVERT: G 89 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7974 (tm-30) REVERT: G 168 GLU cc_start: 0.7899 (pp20) cc_final: 0.7653 (pp20) REVERT: I 1 MET cc_start: 0.6795 (ppp) cc_final: 0.6501 (ppp) REVERT: K 13 ARG cc_start: 0.8442 (mmt90) cc_final: 0.7754 (mpt180) REVERT: K 16 TYR cc_start: 0.8242 (m-80) cc_final: 0.7770 (m-80) REVERT: K 67 ASP cc_start: 0.9040 (p0) cc_final: 0.8434 (p0) REVERT: K 99 ARG cc_start: 0.8733 (ttm170) cc_final: 0.8135 (tpp80) REVERT: K 103 ASN cc_start: 0.9366 (m110) cc_final: 0.9125 (m110) REVERT: K 120 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8800 (mmtt) REVERT: K 121 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7982 (mtmt) REVERT: K 136 GLN cc_start: 0.9577 (mt0) cc_final: 0.9216 (mp10) REVERT: L 6 SER cc_start: 0.9044 (m) cc_final: 0.8805 (m) REVERT: L 14 THR cc_start: 0.9205 (p) cc_final: 0.8966 (t) REVERT: L 53 LYS cc_start: 0.9065 (mptt) cc_final: 0.8829 (mmtt) REVERT: L 71 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6394 (mtt90) REVERT: L 81 GLU cc_start: 0.8503 (pp20) cc_final: 0.8145 (pp20) REVERT: L 92 ASP cc_start: 0.8046 (m-30) cc_final: 0.7486 (m-30) REVERT: L 110 LYS cc_start: 0.9465 (mmtm) cc_final: 0.9196 (mmmt) REVERT: M 6 LEU cc_start: 0.9607 (mt) cc_final: 0.9325 (mp) REVERT: M 50 PHE cc_start: 0.8548 (t80) cc_final: 0.8317 (t80) REVERT: M 59 MET cc_start: 0.7284 (mmp) cc_final: 0.6884 (mmm) REVERT: M 67 PHE cc_start: 0.8263 (p90) cc_final: 0.7974 (p90) REVERT: M 82 ASP cc_start: 0.9019 (m-30) cc_final: 0.8794 (m-30) REVERT: N 31 ASP cc_start: 0.8786 (m-30) cc_final: 0.8560 (m-30) REVERT: N 63 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8207 (tttt) REVERT: N 66 ILE cc_start: 0.9496 (mt) cc_final: 0.9294 (mm) REVERT: N 67 ASN cc_start: 0.8920 (m110) cc_final: 0.8356 (m-40) REVERT: N 85 SER cc_start: 0.9253 (t) cc_final: 0.8951 (p) REVERT: N 105 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7486 (mt-10) REVERT: N 108 TYR cc_start: 0.8508 (t80) cc_final: 0.8199 (t80) REVERT: N 110 ASP cc_start: 0.8804 (t70) cc_final: 0.8215 (t0) REVERT: N 116 ASP cc_start: 0.9541 (m-30) cc_final: 0.9332 (m-30) REVERT: O 23 ASN cc_start: 0.9027 (m-40) cc_final: 0.8778 (m110) REVERT: O 102 ASN cc_start: 0.9339 (m-40) cc_final: 0.9098 (m-40) REVERT: O 107 ASN cc_start: 0.8819 (t0) cc_final: 0.8569 (t0) REVERT: P 9 ASN cc_start: 0.8555 (t0) cc_final: 0.8133 (t0) REVERT: P 59 THR cc_start: 0.9072 (m) cc_final: 0.8814 (p) REVERT: P 64 SER cc_start: 0.9248 (p) cc_final: 0.8999 (m) REVERT: P 98 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7342 (mm-30) REVERT: Q 8 ASP cc_start: 0.9329 (m-30) cc_final: 0.9120 (m-30) REVERT: Q 49 ARG cc_start: 0.8942 (ttt180) cc_final: 0.8304 (mmm-85) REVERT: Q 98 TYR cc_start: 0.8835 (p90) cc_final: 0.8444 (p90) REVERT: R 91 ASP cc_start: 0.8156 (p0) cc_final: 0.7726 (p0) REVERT: R 102 ASP cc_start: 0.8543 (t0) cc_final: 0.8087 (t0) REVERT: S 26 LYS cc_start: 0.9519 (ttpp) cc_final: 0.9178 (ttpp) REVERT: S 65 LEU cc_start: 0.9282 (mt) cc_final: 0.8598 (mt) REVERT: S 66 GLU cc_start: 0.7718 (pm20) cc_final: 0.7426 (pm20) REVERT: S 69 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8659 (mtmm) REVERT: S 86 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8423 (mtpp) REVERT: T 13 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8131 (mtmm) REVERT: T 16 TYR cc_start: 0.9148 (m-80) cc_final: 0.8944 (m-80) REVERT: T 25 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7605 (mtt-85) REVERT: T 29 ASP cc_start: 0.8005 (m-30) cc_final: 0.7774 (m-30) REVERT: T 60 SER cc_start: 0.9270 (t) cc_final: 0.8884 (p) REVERT: T 64 ASN cc_start: 0.8872 (m-40) cc_final: 0.8648 (m-40) REVERT: T 97 GLN cc_start: 0.8803 (mt0) cc_final: 0.8566 (mm110) REVERT: T 108 SER cc_start: 0.8749 (p) cc_final: 0.8358 (m) REVERT: U 6 ASP cc_start: 0.8667 (t0) cc_final: 0.8082 (t0) REVERT: U 37 SER cc_start: 0.9191 (m) cc_final: 0.8667 (m) REVERT: U 70 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7004 (ptt-90) REVERT: U 81 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8288 (mtt180) REVERT: V 1 MET cc_start: 0.9091 (ptm) cc_final: 0.8642 (ptm) REVERT: V 39 ASN cc_start: 0.9108 (t0) cc_final: 0.8413 (t0) REVERT: V 41 ILE cc_start: 0.9191 (pt) cc_final: 0.8886 (pt) REVERT: V 62 GLN cc_start: 0.8103 (mm110) cc_final: 0.7778 (mp-120) REVERT: V 97 ILE cc_start: 0.9094 (mt) cc_final: 0.8826 (tp) REVERT: W 43 ASP cc_start: 0.8187 (m-30) cc_final: 0.7667 (p0) REVERT: W 45 GLN cc_start: 0.8114 (mp10) cc_final: 0.7631 (mm-40) REVERT: W 93 GLN cc_start: 0.8709 (mt0) cc_final: 0.7363 (mt0) REVERT: W 156 GLN cc_start: 0.9297 (mt0) cc_final: 0.8849 (tp40) REVERT: W 161 GLN cc_start: 0.8655 (mp10) cc_final: 0.8124 (mp10) REVERT: W 169 ASN cc_start: 0.9511 (m-40) cc_final: 0.9203 (m-40) REVERT: X 11 ARG cc_start: 0.8574 (ptp90) cc_final: 0.8222 (ttm110) REVERT: X 44 HIS cc_start: 0.9138 (t-90) cc_final: 0.8849 (t70) REVERT: X 76 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8449 (mttt) REVERT: Y 57 LYS cc_start: 0.9255 (tttt) cc_final: 0.8989 (ttmm) REVERT: Z 15 ASP cc_start: 0.9067 (p0) cc_final: 0.8393 (p0) REVERT: Z 16 ASP cc_start: 0.9295 (p0) cc_final: 0.8635 (p0) REVERT: Z 20 ASP cc_start: 0.9058 (m-30) cc_final: 0.8563 (m-30) REVERT: Z 27 GLU cc_start: 0.8495 (tp30) cc_final: 0.8253 (tp30) REVERT: Z 29 LEU cc_start: 0.9459 (tp) cc_final: 0.9196 (tt) REVERT: Z 52 GLN cc_start: 0.8847 (mt0) cc_final: 0.8496 (mm-40) REVERT: a 3 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7983 (mm-30) REVERT: a 7 THR cc_start: 0.8884 (m) cc_final: 0.8160 (p) REVERT: a 8 GLN cc_start: 0.8699 (tt0) cc_final: 0.8323 (tt0) REVERT: a 11 SER cc_start: 0.9187 (t) cc_final: 0.8448 (m) REVERT: a 33 GLN cc_start: 0.8352 (mt0) cc_final: 0.7887 (mt0) REVERT: b 19 GLN cc_start: 0.8835 (mm110) cc_final: 0.7980 (mp10) REVERT: c 16 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8372 (mm-30) REVERT: c 27 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8038 (tmmt) REVERT: c 39 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7479 (ttpt) REVERT: c 50 PRO cc_start: 0.8557 (Cg_exo) cc_final: 0.7822 (Cg_endo) REVERT: d 8 PHE cc_start: 0.8784 (t80) cc_final: 0.8522 (t80) REVERT: f 2 LYS cc_start: 0.9467 (mttt) cc_final: 0.9176 (mttm) REVERT: f 8 LYS cc_start: 0.9290 (mttt) cc_final: 0.9004 (mttp) REVERT: f 29 ASP cc_start: 0.8891 (t0) cc_final: 0.8673 (t0) outliers start: 0 outliers final: 0 residues processed: 1281 average time/residue: 1.0217 time to fit residues: 2156.5575 Evaluate side-chains 939 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 939 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 6.9990 chunk 499 optimal weight: 0.7980 chunk 277 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 598 optimal weight: 7.9990 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 145 HIS D 172 ASN ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN G 75 ASN G 144 GLN J 32 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 4 GLN L 89 ASN ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS Q 79 ASN S 88 GLN T 48 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 ASN ** V 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN X 50 ASN Y 34 GLN Y 50 ASN Z 44 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 GLN ** g 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 105356 Z= 0.444 Angle : 0.717 14.935 158464 Z= 0.364 Chirality : 0.041 0.342 20367 Planarity : 0.006 0.103 8077 Dihedral : 24.779 179.994 54712 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 0.28 % Allowed : 6.29 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 3463 helix: 0.19 (0.16), residues: 961 sheet: -0.06 (0.18), residues: 791 loop : -0.76 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.010 0.002 HIS a 52 PHE 0.027 0.003 PHE D 17 TYR 0.016 0.002 TYR g 9 ARG 0.018 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1080 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 ASP cc_start: 0.9131 (t0) cc_final: 0.8859 (t0) REVERT: C 51 THR cc_start: 0.9071 (m) cc_final: 0.8776 (t) REVERT: C 115 ASP cc_start: 0.8284 (m-30) cc_final: 0.7810 (m-30) REVERT: C 118 GLU cc_start: 0.8998 (pm20) cc_final: 0.8793 (pm20) REVERT: C 124 ASP cc_start: 0.8417 (t0) cc_final: 0.7823 (t0) REVERT: C 146 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7851 (mt-10) REVERT: C 204 ILE cc_start: 0.9408 (mp) cc_final: 0.9186 (mp) REVERT: D 15 GLN cc_start: 0.9341 (pt0) cc_final: 0.8958 (pt0) REVERT: D 54 TYR cc_start: 0.8634 (t80) cc_final: 0.8257 (t80) REVERT: D 69 GLN cc_start: 0.8953 (mt0) cc_final: 0.8665 (mm-40) REVERT: D 99 GLN cc_start: 0.9292 (tt0) cc_final: 0.9070 (tt0) REVERT: D 166 MET cc_start: 0.8316 (mtp) cc_final: 0.7709 (mtp) REVERT: D 179 ASN cc_start: 0.9155 (m-40) cc_final: 0.8739 (m110) REVERT: D 186 ASP cc_start: 0.8957 (t0) cc_final: 0.8242 (t0) REVERT: D 202 ASN cc_start: 0.8991 (m-40) cc_final: 0.8654 (m-40) REVERT: D 210 SER cc_start: 0.8910 (t) cc_final: 0.8368 (p) REVERT: E 19 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8001 (mm-30) REVERT: E 76 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8891 (mm110) REVERT: E 84 PHE cc_start: 0.8200 (m-80) cc_final: 0.7943 (m-80) REVERT: E 106 MET cc_start: 0.9003 (mmm) cc_final: 0.8582 (mmt) REVERT: E 158 ILE cc_start: 0.9369 (mp) cc_final: 0.9097 (mm) REVERT: F 58 ASN cc_start: 0.9433 (m-40) cc_final: 0.9157 (m110) REVERT: F 71 LYS cc_start: 0.8652 (pptt) cc_final: 0.8328 (pptt) REVERT: F 139 LEU cc_start: 0.9783 (mt) cc_final: 0.9474 (tp) REVERT: F 154 ASP cc_start: 0.7865 (p0) cc_final: 0.7599 (p0) REVERT: F 170 ASP cc_start: 0.7086 (m-30) cc_final: 0.6715 (m-30) REVERT: F 185 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8530 (mmmt) REVERT: G 35 LEU cc_start: 0.8633 (tt) cc_final: 0.8243 (tt) REVERT: G 36 ASP cc_start: 0.9238 (m-30) cc_final: 0.8746 (t0) REVERT: G 89 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8064 (tm-30) REVERT: G 138 ASP cc_start: 0.8946 (t0) cc_final: 0.8184 (t0) REVERT: G 141 LYS cc_start: 0.9309 (mtpt) cc_final: 0.9089 (mttp) REVERT: K 16 TYR cc_start: 0.8859 (m-80) cc_final: 0.8258 (m-80) REVERT: K 22 ASP cc_start: 0.8653 (m-30) cc_final: 0.8263 (t70) REVERT: K 67 ASP cc_start: 0.8511 (p0) cc_final: 0.7824 (p0) REVERT: K 71 LYS cc_start: 0.9299 (mtmm) cc_final: 0.9067 (mtmm) REVERT: K 87 ARG cc_start: 0.8877 (ptp-110) cc_final: 0.8590 (ptp-110) REVERT: K 99 ARG cc_start: 0.8863 (ttm170) cc_final: 0.8304 (tpp80) REVERT: K 103 ASN cc_start: 0.9363 (m110) cc_final: 0.9038 (m110) REVERT: K 120 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8932 (mmtt) REVERT: K 136 GLN cc_start: 0.9626 (mt0) cc_final: 0.9258 (mp10) REVERT: L 6 SER cc_start: 0.8972 (m) cc_final: 0.8721 (m) REVERT: L 9 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8687 (mtpp) REVERT: L 18 GLU cc_start: 0.7895 (pp20) cc_final: 0.7488 (pp20) REVERT: L 53 LYS cc_start: 0.9235 (mptt) cc_final: 0.8974 (mmtt) REVERT: L 81 GLU cc_start: 0.8445 (pp20) cc_final: 0.7831 (pp20) REVERT: L 90 ASP cc_start: 0.8158 (p0) cc_final: 0.7719 (p0) REVERT: L 92 ASP cc_start: 0.7678 (m-30) cc_final: 0.6333 (m-30) REVERT: L 120 GLU cc_start: 0.8919 (tp30) cc_final: 0.8669 (tp30) REVERT: M 67 PHE cc_start: 0.8637 (p90) cc_final: 0.8130 (p90) REVERT: M 68 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8087 (mtmt) REVERT: M 69 ASN cc_start: 0.9005 (t0) cc_final: 0.8760 (t0) REVERT: M 70 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.7978 (tmm-80) REVERT: M 123 ASP cc_start: 0.9189 (p0) cc_final: 0.8976 (p0) REVERT: N 31 ASP cc_start: 0.8743 (m-30) cc_final: 0.8499 (m-30) REVERT: N 55 ASN cc_start: 0.9241 (m-40) cc_final: 0.8892 (m-40) REVERT: N 63 LYS cc_start: 0.8465 (ttpp) cc_final: 0.7945 (tttt) REVERT: N 67 ASN cc_start: 0.8995 (m110) cc_final: 0.8143 (m-40) REVERT: N 105 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7533 (mt-10) REVERT: N 116 ASP cc_start: 0.9522 (m-30) cc_final: 0.9281 (m-30) REVERT: O 67 MET cc_start: 0.9335 (mtm) cc_final: 0.8890 (mtm) REVERT: O 72 ASP cc_start: 0.9014 (t0) cc_final: 0.8795 (t0) REVERT: O 102 ASN cc_start: 0.9439 (m-40) cc_final: 0.9085 (m-40) REVERT: O 107 ASN cc_start: 0.8916 (t0) cc_final: 0.8519 (t0) REVERT: O 110 MET cc_start: 0.8886 (mmm) cc_final: 0.8607 (mmm) REVERT: P 8 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7124 (tm-30) REVERT: P 67 GLU cc_start: 0.8942 (tp30) cc_final: 0.8694 (tp30) REVERT: P 98 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7756 (mm-30) REVERT: Q 49 ARG cc_start: 0.9174 (ttt180) cc_final: 0.8757 (mmm-85) REVERT: Q 82 HIS cc_start: 0.8525 (m-70) cc_final: 0.8141 (t-90) REVERT: Q 84 ASP cc_start: 0.8552 (m-30) cc_final: 0.8282 (m-30) REVERT: Q 99 LEU cc_start: 0.9374 (mt) cc_final: 0.9133 (mt) REVERT: Q 103 ARG cc_start: 0.8506 (mpp80) cc_final: 0.8116 (mpp80) REVERT: R 22 LYS cc_start: 0.9310 (mtpp) cc_final: 0.9090 (mttm) REVERT: R 56 GLU cc_start: 0.8074 (mp0) cc_final: 0.7824 (mp0) REVERT: R 84 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8992 (ttpt) REVERT: R 91 ASP cc_start: 0.8225 (p0) cc_final: 0.7532 (p0) REVERT: R 102 ASP cc_start: 0.8911 (t0) cc_final: 0.8479 (t0) REVERT: S 66 GLU cc_start: 0.8166 (pm20) cc_final: 0.7842 (pm20) REVERT: S 84 TYR cc_start: 0.9143 (t80) cc_final: 0.8632 (t80) REVERT: S 86 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8593 (mtpp) REVERT: T 16 TYR cc_start: 0.9300 (m-80) cc_final: 0.9091 (m-80) REVERT: T 29 ASP cc_start: 0.8257 (m-30) cc_final: 0.8008 (m-30) REVERT: T 37 GLU cc_start: 0.8828 (mp0) cc_final: 0.8618 (mp0) REVERT: T 71 LEU cc_start: 0.9559 (mm) cc_final: 0.9329 (mp) REVERT: T 97 GLN cc_start: 0.9133 (mt0) cc_final: 0.8615 (mm110) REVERT: T 108 SER cc_start: 0.8994 (p) cc_final: 0.8650 (m) REVERT: T 115 GLU cc_start: 0.7089 (tp30) cc_final: 0.6678 (tp30) REVERT: U 6 ASP cc_start: 0.8947 (t0) cc_final: 0.8203 (t0) REVERT: U 27 ASN cc_start: 0.9038 (m110) cc_final: 0.8790 (m-40) REVERT: U 37 SER cc_start: 0.8846 (m) cc_final: 0.8517 (m) REVERT: U 55 ASP cc_start: 0.8676 (m-30) cc_final: 0.8393 (m-30) REVERT: U 68 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8360 (ttp-170) REVERT: U 70 ARG cc_start: 0.7523 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: U 76 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8410 (mtt-85) REVERT: V 39 ASN cc_start: 0.9150 (t0) cc_final: 0.8422 (t0) REVERT: V 41 ILE cc_start: 0.9300 (pt) cc_final: 0.8866 (pt) REVERT: W 43 ASP cc_start: 0.8118 (m-30) cc_final: 0.7363 (p0) REVERT: W 45 GLN cc_start: 0.8341 (mp10) cc_final: 0.7613 (mm-40) REVERT: W 84 ASP cc_start: 0.8610 (t0) cc_final: 0.8391 (t0) REVERT: W 93 GLN cc_start: 0.9034 (mt0) cc_final: 0.7846 (mt0) REVERT: W 126 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8348 (tm-30) REVERT: W 156 GLN cc_start: 0.9204 (mt0) cc_final: 0.8829 (tp40) REVERT: W 161 GLN cc_start: 0.8460 (mp10) cc_final: 0.7813 (mp10) REVERT: X 15 ASP cc_start: 0.9053 (t0) cc_final: 0.8701 (t0) REVERT: X 19 GLN cc_start: 0.8177 (mp10) cc_final: 0.7836 (mp10) REVERT: X 32 LYS cc_start: 0.7634 (mttt) cc_final: 0.6660 (mttt) REVERT: X 44 HIS cc_start: 0.9107 (t-90) cc_final: 0.8765 (t70) REVERT: X 73 ARG cc_start: 0.8309 (mtp-110) cc_final: 0.8009 (ttp-110) REVERT: X 76 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8532 (mttp) REVERT: Y 6 ASP cc_start: 0.9259 (m-30) cc_final: 0.8967 (m-30) REVERT: Y 57 LYS cc_start: 0.9326 (tttt) cc_final: 0.8999 (ttmm) REVERT: Z 5 THR cc_start: 0.8850 (t) cc_final: 0.8542 (t) REVERT: Z 15 ASP cc_start: 0.9332 (p0) cc_final: 0.8696 (p0) REVERT: Z 19 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9123 (mtmm) REVERT: Z 28 GLU cc_start: 0.8552 (pm20) cc_final: 0.8109 (pm20) REVERT: Z 29 LEU cc_start: 0.9418 (tp) cc_final: 0.9188 (tt) REVERT: Z 36 MET cc_start: 0.8956 (mmt) cc_final: 0.8739 (mmt) REVERT: Z 41 LEU cc_start: 0.9439 (tp) cc_final: 0.9180 (tp) REVERT: Z 52 GLN cc_start: 0.9003 (mt0) cc_final: 0.8527 (mm-40) REVERT: a 7 THR cc_start: 0.8997 (m) cc_final: 0.8430 (p) REVERT: a 8 GLN cc_start: 0.8730 (tt0) cc_final: 0.8402 (tt0) REVERT: a 11 SER cc_start: 0.9338 (t) cc_final: 0.9027 (m) REVERT: a 33 GLN cc_start: 0.8473 (mt0) cc_final: 0.8103 (mt0) REVERT: b 8 MET cc_start: 0.8779 (tpp) cc_final: 0.8440 (tpp) REVERT: b 12 ASN cc_start: 0.8189 (m110) cc_final: 0.7483 (m110) REVERT: b 49 LEU cc_start: 0.9532 (mm) cc_final: 0.9298 (mm) REVERT: c 16 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8473 (mm-30) REVERT: c 39 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7648 (ttpt) REVERT: c 50 PRO cc_start: 0.8525 (Cg_exo) cc_final: 0.7720 (Cg_endo) REVERT: d 8 PHE cc_start: 0.8917 (t80) cc_final: 0.8582 (t80) REVERT: d 12 ASN cc_start: 0.9147 (m110) cc_final: 0.8943 (m110) REVERT: f 2 LYS cc_start: 0.9495 (mttt) cc_final: 0.9192 (mttm) REVERT: f 8 LYS cc_start: 0.9319 (mttt) cc_final: 0.9037 (mttp) REVERT: f 19 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6843 (mtt-85) REVERT: f 29 ASP cc_start: 0.9129 (t0) cc_final: 0.8841 (t0) REVERT: f 36 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8323 (tm-30) outliers start: 8 outliers final: 2 residues processed: 1083 average time/residue: 0.9695 time to fit residues: 1751.2499 Evaluate side-chains 884 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 882 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 498 optimal weight: 2.9990 chunk 407 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 599 optimal weight: 10.0000 chunk 647 optimal weight: 7.9990 chunk 533 optimal weight: 4.9990 chunk 594 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 480 optimal weight: 0.7980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS C 87 ASN C 129 ASN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN J 32 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 ASN ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN R 94 ASN S 88 GLN ** T 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN Y 50 ASN ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 GLN ** c 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 HIS f 34 GLN g 40 GLN ** g 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 105356 Z= 0.259 Angle : 0.595 11.245 158464 Z= 0.306 Chirality : 0.035 0.299 20367 Planarity : 0.005 0.076 8077 Dihedral : 24.679 178.675 54712 Min Nonbonded Distance : 1.056 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.35 (0.14), residues: 3463 helix: 0.54 (0.17), residues: 959 sheet: 0.00 (0.18), residues: 791 loop : -0.73 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 206 HIS 0.007 0.001 HIS a 52 PHE 0.019 0.002 PHE D 70 TYR 0.019 0.002 TYR R 76 ARG 0.009 0.001 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1058 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8415 (mtm110) REVERT: 3 15 LYS cc_start: 0.8177 (tptp) cc_final: 0.7929 (tptp) REVERT: C 20 ASP cc_start: 0.9146 (t0) cc_final: 0.8893 (t0) REVERT: C 30 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 51 THR cc_start: 0.9127 (m) cc_final: 0.8853 (t) REVERT: C 115 ASP cc_start: 0.8539 (m-30) cc_final: 0.7890 (m-30) REVERT: C 124 ASP cc_start: 0.8497 (t0) cc_final: 0.7838 (t0) REVERT: C 146 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8128 (mt-10) REVERT: C 204 ILE cc_start: 0.9356 (mp) cc_final: 0.9104 (mp) REVERT: D 15 GLN cc_start: 0.9290 (pt0) cc_final: 0.8884 (pt0) REVERT: D 54 TYR cc_start: 0.8452 (t80) cc_final: 0.8090 (t80) REVERT: D 95 TYR cc_start: 0.9138 (m-80) cc_final: 0.8904 (m-10) REVERT: D 99 GLN cc_start: 0.9212 (tt0) cc_final: 0.8345 (mt0) REVERT: D 101 LEU cc_start: 0.9308 (mm) cc_final: 0.9075 (mm) REVERT: D 166 MET cc_start: 0.8183 (mtp) cc_final: 0.7916 (mtp) REVERT: D 179 ASN cc_start: 0.9058 (m110) cc_final: 0.8754 (m110) REVERT: D 186 ASP cc_start: 0.8938 (t0) cc_final: 0.8632 (t0) REVERT: D 202 ASN cc_start: 0.8958 (m-40) cc_final: 0.8626 (m-40) REVERT: D 210 SER cc_start: 0.8948 (t) cc_final: 0.8228 (p) REVERT: E 66 TYR cc_start: 0.8855 (p90) cc_final: 0.8507 (p90) REVERT: E 76 GLN cc_start: 0.9335 (mm-40) cc_final: 0.8806 (mm110) REVERT: F 45 MET cc_start: 0.8603 (mmm) cc_final: 0.8224 (mmt) REVERT: F 58 ASN cc_start: 0.9448 (m-40) cc_final: 0.9186 (m-40) REVERT: F 71 LYS cc_start: 0.8981 (pptt) cc_final: 0.8407 (pptt) REVERT: F 85 LYS cc_start: 0.9666 (mttm) cc_final: 0.9450 (ptmm) REVERT: F 170 ASP cc_start: 0.7236 (m-30) cc_final: 0.6870 (m-30) REVERT: F 185 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8561 (mmmt) REVERT: G 7 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7606 (tm-30) REVERT: G 36 ASP cc_start: 0.9265 (m-30) cc_final: 0.8778 (t0) REVERT: G 89 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 103 ASN cc_start: 0.9190 (m-40) cc_final: 0.8939 (m-40) REVERT: G 138 ASP cc_start: 0.8965 (t0) cc_final: 0.8162 (t0) REVERT: G 141 LYS cc_start: 0.9298 (mtpt) cc_final: 0.9074 (mttp) REVERT: K 16 TYR cc_start: 0.8904 (m-80) cc_final: 0.8429 (m-80) REVERT: K 71 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8962 (mtmm) REVERT: K 99 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8149 (tpp80) REVERT: K 103 ASN cc_start: 0.9326 (m110) cc_final: 0.8996 (m110) REVERT: K 120 LYS cc_start: 0.9326 (mmtt) cc_final: 0.9026 (mmtt) REVERT: K 136 GLN cc_start: 0.9596 (mt0) cc_final: 0.9243 (mp10) REVERT: L 1 MET cc_start: 0.8574 (tpt) cc_final: 0.7896 (tpt) REVERT: L 6 SER cc_start: 0.8977 (m) cc_final: 0.8751 (m) REVERT: L 9 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8655 (mtpp) REVERT: L 17 LYS cc_start: 0.9348 (mptt) cc_final: 0.8913 (mmtm) REVERT: L 18 GLU cc_start: 0.8300 (pp20) cc_final: 0.8039 (pp20) REVERT: L 32 TYR cc_start: 0.8674 (m-10) cc_final: 0.8405 (m-10) REVERT: L 35 ILE cc_start: 0.9445 (mt) cc_final: 0.9115 (mm) REVERT: L 81 GLU cc_start: 0.8458 (pp20) cc_final: 0.7787 (pp20) REVERT: L 90 ASP cc_start: 0.8761 (p0) cc_final: 0.8485 (p0) REVERT: M 68 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8055 (mtmt) REVERT: M 71 PHE cc_start: 0.8906 (m-80) cc_final: 0.8590 (m-80) REVERT: N 55 ASN cc_start: 0.9311 (m-40) cc_final: 0.8947 (m110) REVERT: N 67 ASN cc_start: 0.8953 (m110) cc_final: 0.8236 (m-40) REVERT: N 93 TRP cc_start: 0.8743 (m100) cc_final: 0.7548 (m100) REVERT: N 105 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6805 (mt-10) REVERT: O 27 SER cc_start: 0.9482 (t) cc_final: 0.9253 (t) REVERT: O 67 MET cc_start: 0.9209 (mtm) cc_final: 0.8993 (mtm) REVERT: O 107 ASN cc_start: 0.8819 (t0) cc_final: 0.8483 (t0) REVERT: O 110 MET cc_start: 0.9179 (mmm) cc_final: 0.8549 (mmm) REVERT: P 8 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7170 (tm-30) REVERT: P 67 GLU cc_start: 0.8954 (tp30) cc_final: 0.8610 (tp30) REVERT: P 87 LEU cc_start: 0.9580 (mm) cc_final: 0.9313 (mp) REVERT: P 107 TYR cc_start: 0.8467 (m-80) cc_final: 0.8186 (m-80) REVERT: Q 38 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.7475 (ptt90) REVERT: Q 49 ARG cc_start: 0.9141 (ttt180) cc_final: 0.8915 (mmm-85) REVERT: Q 101 GLU cc_start: 0.8870 (pm20) cc_final: 0.8598 (pm20) REVERT: Q 102 LEU cc_start: 0.9465 (mt) cc_final: 0.9258 (mt) REVERT: R 22 LYS cc_start: 0.9267 (mtpp) cc_final: 0.9021 (mttm) REVERT: R 24 TYR cc_start: 0.8769 (m-10) cc_final: 0.8325 (m-80) REVERT: R 91 ASP cc_start: 0.8269 (p0) cc_final: 0.7656 (p0) REVERT: R 102 ASP cc_start: 0.8835 (t0) cc_final: 0.8399 (t0) REVERT: S 66 GLU cc_start: 0.8196 (pm20) cc_final: 0.7860 (pm20) REVERT: S 84 TYR cc_start: 0.9031 (t80) cc_final: 0.8498 (t80) REVERT: S 86 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8622 (mtpp) REVERT: T 16 TYR cc_start: 0.9292 (m-80) cc_final: 0.9090 (m-80) REVERT: T 29 ASP cc_start: 0.8207 (m-30) cc_final: 0.7950 (m-30) REVERT: T 34 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8158 (mttp) REVERT: T 37 GLU cc_start: 0.8824 (mp0) cc_final: 0.8562 (mp0) REVERT: T 60 SER cc_start: 0.9333 (t) cc_final: 0.8805 (p) REVERT: T 97 GLN cc_start: 0.9121 (mt0) cc_final: 0.8663 (mm110) REVERT: T 108 SER cc_start: 0.9064 (p) cc_final: 0.8776 (m) REVERT: U 6 ASP cc_start: 0.8887 (t0) cc_final: 0.8166 (t0) REVERT: U 24 ILE cc_start: 0.8972 (tt) cc_final: 0.8770 (tt) REVERT: U 27 ASN cc_start: 0.9026 (m110) cc_final: 0.8765 (m-40) REVERT: U 41 GLN cc_start: 0.8450 (mt0) cc_final: 0.7914 (mt0) REVERT: U 68 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8278 (ttm110) REVERT: V 7 ASP cc_start: 0.8181 (m-30) cc_final: 0.7981 (m-30) REVERT: V 12 ILE cc_start: 0.9425 (mp) cc_final: 0.9170 (mp) REVERT: V 39 ASN cc_start: 0.9081 (t0) cc_final: 0.8262 (t0) REVERT: V 62 GLN cc_start: 0.7410 (mp-120) cc_final: 0.7168 (mp-120) REVERT: V 85 TYR cc_start: 0.8907 (m-10) cc_final: 0.8629 (m-10) REVERT: W 32 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7898 (mmmt) REVERT: W 43 ASP cc_start: 0.8063 (m-30) cc_final: 0.7512 (p0) REVERT: W 84 ASP cc_start: 0.8643 (t0) cc_final: 0.8392 (t0) REVERT: W 93 GLN cc_start: 0.9156 (mt0) cc_final: 0.8154 (mt0) REVERT: W 101 GLN cc_start: 0.7782 (pm20) cc_final: 0.7535 (pm20) REVERT: W 161 GLN cc_start: 0.8432 (mp10) cc_final: 0.7821 (mp10) REVERT: X 19 GLN cc_start: 0.8096 (mp10) cc_final: 0.7700 (mp10) REVERT: X 32 LYS cc_start: 0.8021 (mttt) cc_final: 0.6812 (mttt) REVERT: X 35 GLU cc_start: 0.7710 (mp0) cc_final: 0.7424 (mp0) REVERT: X 76 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8482 (mttp) REVERT: Y 6 ASP cc_start: 0.9314 (m-30) cc_final: 0.9028 (m-30) REVERT: Y 57 LYS cc_start: 0.9295 (tttt) cc_final: 0.8958 (ttmm) REVERT: Z 29 LEU cc_start: 0.9403 (tp) cc_final: 0.9163 (tt) REVERT: Z 31 ASN cc_start: 0.9427 (m110) cc_final: 0.8929 (m110) REVERT: Z 52 GLN cc_start: 0.9052 (mt0) cc_final: 0.8545 (mm-40) REVERT: Z 59 THR cc_start: 0.9060 (m) cc_final: 0.8780 (p) REVERT: a 7 THR cc_start: 0.8968 (m) cc_final: 0.8297 (p) REVERT: a 8 GLN cc_start: 0.8819 (tt0) cc_final: 0.8485 (tt0) REVERT: a 11 SER cc_start: 0.9214 (t) cc_final: 0.8504 (p) REVERT: a 21 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9220 (mm-30) REVERT: a 33 GLN cc_start: 0.8506 (mt0) cc_final: 0.8149 (mt0) REVERT: a 48 ASN cc_start: 0.9637 (t0) cc_final: 0.9381 (t0) REVERT: c 16 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8744 (mm-30) REVERT: c 27 LYS cc_start: 0.8580 (ttpt) cc_final: 0.7829 (tmmt) REVERT: c 39 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7755 (ttpt) REVERT: c 50 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.7769 (Cg_endo) REVERT: d 5 LYS cc_start: 0.8975 (tttm) cc_final: 0.8658 (tttm) REVERT: d 9 GLN cc_start: 0.9322 (mm110) cc_final: 0.8954 (mm110) REVERT: f 8 LYS cc_start: 0.9299 (mttt) cc_final: 0.8988 (mttp) REVERT: f 36 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8142 (tm-30) outliers start: 5 outliers final: 1 residues processed: 1058 average time/residue: 0.9764 time to fit residues: 1721.4443 Evaluate side-chains 887 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 886 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 1.9990 chunk 450 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 402 optimal weight: 10.0000 chunk 601 optimal weight: 5.9990 chunk 636 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 570 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN J 32 GLN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 4 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN Q 79 ASN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN T 66 GLN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN ** c 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 105356 Z= 0.365 Angle : 0.654 14.533 158464 Z= 0.335 Chirality : 0.038 0.290 20367 Planarity : 0.005 0.075 8077 Dihedral : 24.617 179.349 54712 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.44 (0.14), residues: 3463 helix: 0.42 (0.17), residues: 951 sheet: 0.06 (0.18), residues: 816 loop : -0.82 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 206 HIS 0.017 0.002 HIS K 96 PHE 0.030 0.002 PHE Z 34 TYR 0.019 0.002 TYR R 76 ARG 0.028 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1019 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8827 (ttp-110) cc_final: 0.8514 (mtm110) REVERT: C 20 ASP cc_start: 0.9098 (t0) cc_final: 0.8862 (t0) REVERT: C 30 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8239 (mm-30) REVERT: C 115 ASP cc_start: 0.8428 (m-30) cc_final: 0.7887 (m-30) REVERT: C 124 ASP cc_start: 0.8495 (t0) cc_final: 0.7918 (t0) REVERT: C 146 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 250 TRP cc_start: 0.9376 (m-90) cc_final: 0.8957 (m-90) REVERT: D 13 MET cc_start: 0.8279 (ttm) cc_final: 0.8030 (ttp) REVERT: D 54 TYR cc_start: 0.8529 (t80) cc_final: 0.8158 (t80) REVERT: D 99 GLN cc_start: 0.9233 (tt0) cc_final: 0.8885 (tt0) REVERT: D 160 VAL cc_start: 0.9270 (t) cc_final: 0.9068 (t) REVERT: D 186 ASP cc_start: 0.8894 (t0) cc_final: 0.8321 (t0) REVERT: D 202 ASN cc_start: 0.8935 (m-40) cc_final: 0.8524 (m-40) REVERT: D 210 SER cc_start: 0.8867 (t) cc_final: 0.7976 (m) REVERT: E 106 MET cc_start: 0.8940 (mmt) cc_final: 0.8640 (mmt) REVERT: E 186 TYR cc_start: 0.9354 (t80) cc_final: 0.9038 (t80) REVERT: E 192 ASP cc_start: 0.8781 (m-30) cc_final: 0.8400 (m-30) REVERT: F 58 ASN cc_start: 0.9495 (m-40) cc_final: 0.9260 (m-40) REVERT: F 71 LYS cc_start: 0.8963 (pptt) cc_final: 0.8525 (pptt) REVERT: F 88 GLU cc_start: 0.9015 (tp30) cc_final: 0.8553 (mm-30) REVERT: F 139 LEU cc_start: 0.9677 (mm) cc_final: 0.9371 (pp) REVERT: F 170 ASP cc_start: 0.7417 (m-30) cc_final: 0.7111 (m-30) REVERT: F 185 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8627 (mmmt) REVERT: G 35 LEU cc_start: 0.8646 (tt) cc_final: 0.8280 (tt) REVERT: G 36 ASP cc_start: 0.9239 (m-30) cc_final: 0.8965 (t70) REVERT: G 103 ASN cc_start: 0.9289 (m-40) cc_final: 0.8856 (m-40) REVERT: G 138 ASP cc_start: 0.9010 (t0) cc_final: 0.8410 (t0) REVERT: K 16 TYR cc_start: 0.8907 (m-80) cc_final: 0.8390 (m-80) REVERT: K 71 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8981 (mtmm) REVERT: K 87 ARG cc_start: 0.8913 (ptp-110) cc_final: 0.8645 (ptp-170) REVERT: K 99 ARG cc_start: 0.8943 (ttm170) cc_final: 0.8447 (tpp80) REVERT: K 103 ASN cc_start: 0.9374 (m110) cc_final: 0.9023 (m110) REVERT: K 117 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8693 (tp-100) REVERT: K 120 LYS cc_start: 0.9322 (mmtt) cc_final: 0.9038 (mmtt) REVERT: K 136 GLN cc_start: 0.9609 (mt0) cc_final: 0.9236 (mp10) REVERT: L 1 MET cc_start: 0.8748 (tpp) cc_final: 0.8352 (tpp) REVERT: L 9 LYS cc_start: 0.9248 (ttpp) cc_final: 0.8849 (mtpp) REVERT: L 17 LYS cc_start: 0.9259 (mptt) cc_final: 0.8898 (mptt) REVERT: L 18 GLU cc_start: 0.8301 (pp20) cc_final: 0.7920 (pp20) REVERT: L 32 TYR cc_start: 0.8726 (m-10) cc_final: 0.8281 (m-10) REVERT: L 35 ILE cc_start: 0.9416 (mt) cc_final: 0.9074 (mm) REVERT: L 81 GLU cc_start: 0.8461 (pp20) cc_final: 0.7746 (pp20) REVERT: L 90 ASP cc_start: 0.8827 (p0) cc_final: 0.8471 (p0) REVERT: M 15 GLU cc_start: 0.8521 (tt0) cc_final: 0.8105 (tt0) REVERT: M 35 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8605 (mtt-85) REVERT: M 49 MET cc_start: 0.8561 (pmm) cc_final: 0.8351 (pmm) REVERT: M 68 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8582 (mtmt) REVERT: M 75 TYR cc_start: 0.9367 (m-80) cc_final: 0.9146 (m-80) REVERT: N 31 ASP cc_start: 0.8848 (m-30) cc_final: 0.8576 (m-30) REVERT: N 48 GLU cc_start: 0.8763 (tp30) cc_final: 0.8447 (tp30) REVERT: N 55 ASN cc_start: 0.9327 (m-40) cc_final: 0.9046 (m-40) REVERT: N 67 ASN cc_start: 0.8602 (m110) cc_final: 0.8125 (m-40) REVERT: N 93 TRP cc_start: 0.8834 (m100) cc_final: 0.7425 (m100) REVERT: N 105 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7141 (mt-10) REVERT: O 67 MET cc_start: 0.9264 (mtm) cc_final: 0.9016 (mtm) REVERT: O 107 ASN cc_start: 0.8895 (t0) cc_final: 0.8547 (t0) REVERT: O 110 MET cc_start: 0.8930 (mmm) cc_final: 0.8472 (mmm) REVERT: P 8 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7228 (tm-30) REVERT: P 87 LEU cc_start: 0.9591 (mm) cc_final: 0.9334 (mp) REVERT: Q 40 GLN cc_start: 0.8969 (tp40) cc_final: 0.8719 (tp-100) REVERT: R 22 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8998 (mttm) REVERT: R 91 ASP cc_start: 0.8010 (p0) cc_final: 0.7581 (p0) REVERT: R 102 ASP cc_start: 0.8923 (t0) cc_final: 0.8481 (t0) REVERT: S 14 TYR cc_start: 0.8973 (m-10) cc_final: 0.8769 (m-10) REVERT: S 66 GLU cc_start: 0.8314 (pm20) cc_final: 0.7876 (pm20) REVERT: S 84 TYR cc_start: 0.8924 (t80) cc_final: 0.8495 (t80) REVERT: S 86 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8638 (mtpp) REVERT: T 16 TYR cc_start: 0.9338 (m-80) cc_final: 0.9031 (m-80) REVERT: T 34 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8555 (mttm) REVERT: T 37 GLU cc_start: 0.8847 (mp0) cc_final: 0.8601 (mp0) REVERT: T 60 SER cc_start: 0.9392 (t) cc_final: 0.8861 (p) REVERT: T 97 GLN cc_start: 0.9031 (mt0) cc_final: 0.8684 (mm110) REVERT: T 108 SER cc_start: 0.9058 (p) cc_final: 0.8731 (m) REVERT: T 115 GLU cc_start: 0.7835 (tt0) cc_final: 0.7411 (tt0) REVERT: U 6 ASP cc_start: 0.8928 (t0) cc_final: 0.8151 (t0) REVERT: U 27 ASN cc_start: 0.9029 (m110) cc_final: 0.8803 (m-40) REVERT: U 37 SER cc_start: 0.8922 (m) cc_final: 0.8577 (t) REVERT: U 41 GLN cc_start: 0.8822 (mt0) cc_final: 0.8622 (mt0) REVERT: U 68 ARG cc_start: 0.8735 (ttm110) cc_final: 0.7877 (mtm110) REVERT: U 69 THR cc_start: 0.8847 (m) cc_final: 0.8526 (m) REVERT: U 81 ARG cc_start: 0.8958 (mtt90) cc_final: 0.8757 (mtt180) REVERT: V 7 ASP cc_start: 0.8302 (m-30) cc_final: 0.8022 (m-30) REVERT: V 39 ASN cc_start: 0.9183 (t0) cc_final: 0.8466 (t0) REVERT: V 62 GLN cc_start: 0.7334 (mp-120) cc_final: 0.7112 (mp-120) REVERT: V 72 MET cc_start: 0.8524 (ttm) cc_final: 0.8274 (ttm) REVERT: W 10 LYS cc_start: 0.9120 (tptp) cc_final: 0.8865 (tppt) REVERT: W 70 ASP cc_start: 0.9028 (t70) cc_final: 0.8719 (p0) REVERT: W 84 ASP cc_start: 0.8783 (t0) cc_final: 0.8453 (t0) REVERT: W 93 GLN cc_start: 0.9177 (mt0) cc_final: 0.8220 (mt0) REVERT: W 105 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8332 (mmmt) REVERT: W 161 GLN cc_start: 0.8497 (mp10) cc_final: 0.7885 (mp10) REVERT: W 173 ASP cc_start: 0.9366 (t0) cc_final: 0.9108 (t70) REVERT: W 175 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9199 (mp0) REVERT: W 183 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8084 (tp30) REVERT: X 19 GLN cc_start: 0.8543 (mp10) cc_final: 0.8016 (mp10) REVERT: X 32 LYS cc_start: 0.8120 (mttt) cc_final: 0.7289 (mttt) REVERT: X 35 GLU cc_start: 0.8062 (mp0) cc_final: 0.7373 (mp0) REVERT: X 73 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7749 (ttp-110) REVERT: X 75 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7795 (mtm180) REVERT: X 76 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8527 (mttp) REVERT: Y 6 ASP cc_start: 0.9298 (m-30) cc_final: 0.9036 (m-30) REVERT: Y 37 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: Y 57 LYS cc_start: 0.9351 (tttt) cc_final: 0.8997 (ttmm) REVERT: Z 29 LEU cc_start: 0.9434 (tp) cc_final: 0.9228 (tt) REVERT: Z 31 ASN cc_start: 0.9476 (m110) cc_final: 0.8869 (m110) REVERT: Z 47 LEU cc_start: 0.9436 (mm) cc_final: 0.9220 (mm) REVERT: Z 52 GLN cc_start: 0.9032 (mt0) cc_final: 0.8534 (mm-40) REVERT: a 7 THR cc_start: 0.8931 (m) cc_final: 0.8265 (p) REVERT: a 8 GLN cc_start: 0.8779 (tt0) cc_final: 0.8483 (tt0) REVERT: a 11 SER cc_start: 0.9247 (t) cc_final: 0.8667 (p) REVERT: a 21 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9166 (mm-30) REVERT: a 33 GLN cc_start: 0.8531 (mt0) cc_final: 0.8194 (mt0) REVERT: a 48 ASN cc_start: 0.9650 (t0) cc_final: 0.9420 (t0) REVERT: c 16 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8728 (mm-30) REVERT: c 27 LYS cc_start: 0.8556 (ttpt) cc_final: 0.7770 (tmmt) REVERT: c 39 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8005 (ttpt) REVERT: c 50 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8003 (Cg_endo) REVERT: d 9 GLN cc_start: 0.9257 (mm110) cc_final: 0.8794 (mm110) REVERT: f 8 LYS cc_start: 0.9174 (mttt) cc_final: 0.8921 (mttp) REVERT: f 19 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8237 (mtt180) REVERT: f 36 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8129 (tm-30) outliers start: 2 outliers final: 0 residues processed: 1019 average time/residue: 0.9747 time to fit residues: 1660.1779 Evaluate side-chains 877 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 877 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 0.0980 chunk 361 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 543 optimal weight: 0.9990 chunk 440 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 571 optimal weight: 8.9990 chunk 160 optimal weight: 50.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 80 HIS E 76 GLN E 208 ASN J 32 GLN J 33 HIS K 103 ASN L 3 GLN M 58 HIS ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN N 57 HIS O 23 ASN O 31 HIS ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN T 68 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN Y 50 ASN a 42 GLN c 20 HIS ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 105356 Z= 0.129 Angle : 0.554 10.520 158464 Z= 0.282 Chirality : 0.032 0.301 20367 Planarity : 0.004 0.053 8077 Dihedral : 24.549 179.864 54712 Min Nonbonded Distance : 1.292 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.10 (0.14), residues: 3463 helix: 0.70 (0.17), residues: 954 sheet: 0.35 (0.18), residues: 798 loop : -0.66 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 17 HIS 0.024 0.001 HIS O 31 PHE 0.028 0.002 PHE Z 30 TYR 0.023 0.001 TYR O 47 ARG 0.008 0.001 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1086 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8502 (mtm110) REVERT: 3 15 LYS cc_start: 0.8033 (tptp) cc_final: 0.7791 (tptp) REVERT: 3 18 HIS cc_start: 0.9012 (m90) cc_final: 0.8664 (m90) REVERT: C 20 ASP cc_start: 0.9103 (t0) cc_final: 0.8858 (t0) REVERT: C 30 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 97 TYR cc_start: 0.8874 (m-80) cc_final: 0.8655 (m-10) REVERT: C 109 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 115 ASP cc_start: 0.8611 (m-30) cc_final: 0.8150 (m-30) REVERT: C 124 ASP cc_start: 0.8622 (t0) cc_final: 0.8009 (t0) REVERT: C 146 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7857 (mt-10) REVERT: C 195 GLU cc_start: 0.8635 (pm20) cc_final: 0.8226 (pm20) REVERT: D 18 ASP cc_start: 0.8802 (t0) cc_final: 0.8073 (t70) REVERT: D 34 ASN cc_start: 0.9122 (m110) cc_final: 0.7817 (m-40) REVERT: D 54 TYR cc_start: 0.8265 (t80) cc_final: 0.7826 (t80) REVERT: D 95 TYR cc_start: 0.9043 (m-80) cc_final: 0.8597 (m-10) REVERT: D 111 TYR cc_start: 0.8929 (m-10) cc_final: 0.6955 (m-10) REVERT: D 123 PHE cc_start: 0.8862 (t80) cc_final: 0.8499 (t80) REVERT: D 202 ASN cc_start: 0.8848 (m-40) cc_final: 0.8509 (m-40) REVERT: D 210 SER cc_start: 0.8701 (t) cc_final: 0.8225 (t) REVERT: E 19 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7986 (tp30) REVERT: E 68 GLN cc_start: 0.8691 (tp40) cc_final: 0.8468 (tp40) REVERT: E 76 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8018 (mm110) REVERT: E 106 MET cc_start: 0.8930 (mmt) cc_final: 0.8470 (mmt) REVERT: E 158 ILE cc_start: 0.9341 (mp) cc_final: 0.8784 (mm) REVERT: E 192 ASP cc_start: 0.8729 (m-30) cc_final: 0.8422 (m-30) REVERT: F 58 ASN cc_start: 0.9515 (m-40) cc_final: 0.9221 (m110) REVERT: F 71 LYS cc_start: 0.8929 (pptt) cc_final: 0.8507 (pptt) REVERT: F 85 LYS cc_start: 0.9551 (pttt) cc_final: 0.8873 (pttp) REVERT: F 88 GLU cc_start: 0.9048 (tp30) cc_final: 0.8662 (mm-30) REVERT: F 129 PHE cc_start: 0.7669 (m-80) cc_final: 0.7416 (m-80) REVERT: F 139 LEU cc_start: 0.9680 (mm) cc_final: 0.9344 (pp) REVERT: F 170 ASP cc_start: 0.7948 (m-30) cc_final: 0.7608 (m-30) REVERT: G 36 ASP cc_start: 0.9339 (m-30) cc_final: 0.8926 (t0) REVERT: G 103 ASN cc_start: 0.9277 (m-40) cc_final: 0.8911 (m-40) REVERT: G 138 ASP cc_start: 0.8814 (t0) cc_final: 0.8493 (t0) REVERT: K 16 TYR cc_start: 0.8873 (m-80) cc_final: 0.8484 (m-80) REVERT: K 71 LYS cc_start: 0.9271 (mtmm) cc_final: 0.8949 (mtmm) REVERT: K 99 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8388 (tpp80) REVERT: K 103 ASN cc_start: 0.9425 (m-40) cc_final: 0.9180 (m110) REVERT: K 117 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8485 (tp-100) REVERT: K 120 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8987 (mmtt) REVERT: K 136 GLN cc_start: 0.9563 (mt0) cc_final: 0.9244 (mp10) REVERT: L 1 MET cc_start: 0.8717 (tpp) cc_final: 0.8147 (tpp) REVERT: L 9 LYS cc_start: 0.9213 (ttpp) cc_final: 0.8820 (mtpp) REVERT: L 14 THR cc_start: 0.9368 (p) cc_final: 0.9044 (p) REVERT: L 17 LYS cc_start: 0.9207 (mptt) cc_final: 0.8655 (mmtt) REVERT: L 18 GLU cc_start: 0.8120 (pp20) cc_final: 0.7639 (pp20) REVERT: L 32 TYR cc_start: 0.8594 (m-10) cc_final: 0.8047 (m-10) REVERT: L 35 ILE cc_start: 0.9333 (mt) cc_final: 0.9003 (mm) REVERT: L 45 ASP cc_start: 0.9293 (t70) cc_final: 0.8967 (t0) REVERT: L 81 GLU cc_start: 0.8507 (pp20) cc_final: 0.7705 (pp20) REVERT: L 90 ASP cc_start: 0.9036 (p0) cc_final: 0.8656 (p0) REVERT: L 120 GLU cc_start: 0.8779 (tp30) cc_final: 0.8557 (tp30) REVERT: M 35 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8640 (mtt-85) REVERT: N 52 ILE cc_start: 0.9436 (tp) cc_final: 0.9221 (pt) REVERT: N 55 ASN cc_start: 0.9313 (m110) cc_final: 0.8938 (m-40) REVERT: N 63 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8223 (tttt) REVERT: N 67 ASN cc_start: 0.8847 (m110) cc_final: 0.8309 (m-40) REVERT: N 81 THR cc_start: 0.9301 (p) cc_final: 0.9034 (p) REVERT: N 93 TRP cc_start: 0.8584 (m100) cc_final: 0.7336 (m100) REVERT: N 98 LYS cc_start: 0.8835 (mttt) cc_final: 0.8583 (mttm) REVERT: N 105 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6138 (mt-10) REVERT: N 110 ASP cc_start: 0.8781 (t70) cc_final: 0.8532 (t70) REVERT: N 132 VAL cc_start: 0.9334 (t) cc_final: 0.9030 (m) REVERT: O 67 MET cc_start: 0.9122 (mtm) cc_final: 0.8881 (mtm) REVERT: O 107 ASN cc_start: 0.8780 (t0) cc_final: 0.8512 (t0) REVERT: P 8 GLN cc_start: 0.7632 (tm-30) cc_final: 0.6975 (tm-30) REVERT: P 46 HIS cc_start: 0.8885 (m-70) cc_final: 0.7371 (m-70) REVERT: P 51 LEU cc_start: 0.9405 (mt) cc_final: 0.9095 (mt) REVERT: P 93 LYS cc_start: 0.9406 (ptpp) cc_final: 0.9133 (pttm) REVERT: P 98 GLU cc_start: 0.8499 (tp30) cc_final: 0.7901 (tp30) REVERT: P 126 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9035 (mmmt) REVERT: Q 2 ASN cc_start: 0.8690 (t0) cc_final: 0.8240 (p0) REVERT: Q 5 ASP cc_start: 0.8210 (p0) cc_final: 0.7966 (p0) REVERT: Q 40 GLN cc_start: 0.9010 (tp40) cc_final: 0.8403 (tp-100) REVERT: Q 93 ARG cc_start: 0.7395 (mpt180) cc_final: 0.7084 (mmt180) REVERT: R 3 ARG cc_start: 0.8499 (ttt90) cc_final: 0.8275 (ttt90) REVERT: R 22 LYS cc_start: 0.9263 (mtpp) cc_final: 0.8993 (mttm) REVERT: R 24 TYR cc_start: 0.8965 (m-10) cc_final: 0.8334 (m-80) REVERT: R 73 ASP cc_start: 0.9030 (t70) cc_final: 0.8706 (t0) REVERT: R 91 ASP cc_start: 0.7933 (p0) cc_final: 0.7512 (p0) REVERT: R 102 ASP cc_start: 0.8773 (t0) cc_final: 0.8319 (t0) REVERT: S 9 THR cc_start: 0.9547 (t) cc_final: 0.9114 (p) REVERT: S 66 GLU cc_start: 0.8298 (pm20) cc_final: 0.7727 (pm20) REVERT: S 84 TYR cc_start: 0.8813 (t80) cc_final: 0.8509 (t80) REVERT: T 7 PHE cc_start: 0.9029 (m-80) cc_final: 0.8768 (m-80) REVERT: T 13 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8377 (mtmm) REVERT: T 16 TYR cc_start: 0.9260 (m-80) cc_final: 0.9049 (m-80) REVERT: T 37 GLU cc_start: 0.8745 (mp0) cc_final: 0.8412 (mp0) REVERT: T 41 ASP cc_start: 0.9073 (m-30) cc_final: 0.8816 (m-30) REVERT: T 60 SER cc_start: 0.9337 (t) cc_final: 0.8467 (p) REVERT: T 64 ASN cc_start: 0.8698 (m-40) cc_final: 0.8209 (m110) REVERT: T 80 THR cc_start: 0.8278 (p) cc_final: 0.7839 (t) REVERT: T 115 GLU cc_start: 0.8116 (tt0) cc_final: 0.7883 (tp30) REVERT: U 6 ASP cc_start: 0.8774 (t0) cc_final: 0.8142 (t0) REVERT: U 63 GLN cc_start: 0.8845 (mp-120) cc_final: 0.8440 (pm20) REVERT: U 68 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8082 (mtm110) REVERT: U 73 PHE cc_start: 0.8788 (m-80) cc_final: 0.8577 (m-10) REVERT: V 7 ASP cc_start: 0.8106 (m-30) cc_final: 0.7857 (m-30) REVERT: V 39 ASN cc_start: 0.9063 (t0) cc_final: 0.8464 (t0) REVERT: V 41 ILE cc_start: 0.9240 (pt) cc_final: 0.8896 (tp) REVERT: V 85 TYR cc_start: 0.8967 (m-10) cc_final: 0.8388 (m-10) REVERT: W 10 LYS cc_start: 0.9279 (tptp) cc_final: 0.8997 (tppt) REVERT: W 43 ASP cc_start: 0.8346 (m-30) cc_final: 0.7572 (p0) REVERT: W 45 GLN cc_start: 0.8926 (mp10) cc_final: 0.8359 (mm110) REVERT: W 54 PHE cc_start: 0.9281 (t80) cc_final: 0.8983 (t80) REVERT: W 70 ASP cc_start: 0.8943 (t70) cc_final: 0.8675 (p0) REVERT: W 84 ASP cc_start: 0.8638 (t0) cc_final: 0.8418 (t0) REVERT: W 93 GLN cc_start: 0.9154 (mt0) cc_final: 0.8304 (mt0) REVERT: W 126 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7840 (tm-30) REVERT: W 143 GLN cc_start: 0.8536 (pp30) cc_final: 0.8128 (pp30) REVERT: W 161 GLN cc_start: 0.8418 (mp10) cc_final: 0.7796 (mp10) REVERT: W 173 ASP cc_start: 0.9281 (t0) cc_final: 0.8999 (t70) REVERT: W 175 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9193 (mp0) REVERT: W 183 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8111 (tp30) REVERT: X 19 GLN cc_start: 0.8527 (mp10) cc_final: 0.8037 (mp10) REVERT: X 35 GLU cc_start: 0.7574 (mp0) cc_final: 0.7364 (mp0) REVERT: X 44 HIS cc_start: 0.9213 (t-90) cc_final: 0.8994 (t70) REVERT: X 76 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8334 (mttp) REVERT: Y 6 ASP cc_start: 0.9303 (m-30) cc_final: 0.9040 (m-30) REVERT: Y 37 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8069 (mmm-85) REVERT: Y 57 LYS cc_start: 0.9279 (tttt) cc_final: 0.8992 (ttmm) REVERT: Z 21 LYS cc_start: 0.9558 (ttmm) cc_final: 0.8998 (tppt) REVERT: Z 31 ASN cc_start: 0.9382 (m110) cc_final: 0.8920 (m-40) REVERT: Z 47 LEU cc_start: 0.9471 (mm) cc_final: 0.9073 (mm) REVERT: Z 51 ARG cc_start: 0.8346 (mtm110) cc_final: 0.8019 (mtm110) REVERT: Z 52 GLN cc_start: 0.9009 (mt0) cc_final: 0.8501 (mm-40) REVERT: Z 59 THR cc_start: 0.8903 (m) cc_final: 0.8586 (p) REVERT: a 7 THR cc_start: 0.8932 (m) cc_final: 0.8295 (p) REVERT: a 8 GLN cc_start: 0.8822 (tt0) cc_final: 0.8542 (tt0) REVERT: a 21 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9099 (mm-30) REVERT: a 33 GLN cc_start: 0.8546 (mt0) cc_final: 0.8126 (mt0) REVERT: b 8 MET cc_start: 0.8799 (tpp) cc_final: 0.8573 (tpp) REVERT: c 16 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8680 (mm-30) REVERT: c 27 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8210 (tttm) REVERT: c 39 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7707 (ttpt) REVERT: c 50 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.7890 (Cg_endo) REVERT: c 52 LYS cc_start: 0.7986 (tptp) cc_final: 0.7722 (mmmt) REVERT: d 9 GLN cc_start: 0.9270 (mm110) cc_final: 0.8763 (mm110) REVERT: f 8 LYS cc_start: 0.9114 (mttt) cc_final: 0.8769 (mttp) REVERT: f 36 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7899 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1086 average time/residue: 0.9873 time to fit residues: 1776.1341 Evaluate side-chains 932 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 932 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 20.0000 chunk 573 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 7.9990 chunk 529 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN G 169 GLN J 32 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN R 94 ASN S 88 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 ASN V 44 HIS ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN Z 44 ASN a 42 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 105356 Z= 0.453 Angle : 0.704 15.348 158464 Z= 0.358 Chirality : 0.040 0.302 20367 Planarity : 0.005 0.059 8077 Dihedral : 24.542 179.816 54712 Min Nonbonded Distance : 0.987 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.50 (0.14), residues: 3463 helix: 0.45 (0.17), residues: 951 sheet: 0.00 (0.18), residues: 834 loop : -0.91 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 45 HIS 0.009 0.002 HIS a 52 PHE 0.031 0.002 PHE R 57 TYR 0.019 0.002 TYR D 95 ARG 0.013 0.001 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 998 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8552 (mtm110) REVERT: C 20 ASP cc_start: 0.9110 (t0) cc_final: 0.8884 (t0) REVERT: C 30 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 109 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8879 (tm-30) REVERT: C 115 ASP cc_start: 0.8436 (m-30) cc_final: 0.8025 (m-30) REVERT: C 124 ASP cc_start: 0.8728 (t0) cc_final: 0.8114 (t0) REVERT: C 146 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 195 GLU cc_start: 0.8673 (pm20) cc_final: 0.8444 (pm20) REVERT: C 250 TRP cc_start: 0.9391 (m-90) cc_final: 0.8840 (m-90) REVERT: D 22 LYS cc_start: 0.9244 (mtmm) cc_final: 0.8898 (mtmm) REVERT: D 34 ASN cc_start: 0.8739 (m110) cc_final: 0.7995 (m-40) REVERT: D 54 TYR cc_start: 0.8552 (t80) cc_final: 0.7889 (t80) REVERT: D 99 GLN cc_start: 0.9147 (tt0) cc_final: 0.8605 (tt0) REVERT: D 202 ASN cc_start: 0.8915 (m-40) cc_final: 0.8466 (m-40) REVERT: D 210 SER cc_start: 0.8776 (t) cc_final: 0.7822 (m) REVERT: E 19 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8057 (tp30) REVERT: E 66 TYR cc_start: 0.8967 (p90) cc_final: 0.8603 (p90) REVERT: E 68 GLN cc_start: 0.8713 (tp40) cc_final: 0.8443 (tp40) REVERT: E 76 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8272 (mm110) REVERT: E 106 MET cc_start: 0.8966 (mmt) cc_final: 0.8727 (mmt) REVERT: E 192 ASP cc_start: 0.8442 (m-30) cc_final: 0.8167 (m-30) REVERT: E 193 ASP cc_start: 0.8073 (m-30) cc_final: 0.7753 (m-30) REVERT: F 58 ASN cc_start: 0.9506 (m110) cc_final: 0.9282 (m-40) REVERT: F 71 LYS cc_start: 0.8877 (pptt) cc_final: 0.8547 (pptt) REVERT: F 121 PHE cc_start: 0.8533 (t80) cc_final: 0.8222 (t80) REVERT: F 170 ASP cc_start: 0.7416 (m-30) cc_final: 0.7170 (m-30) REVERT: F 185 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8554 (mmmt) REVERT: G 36 ASP cc_start: 0.9313 (m-30) cc_final: 0.9041 (t70) REVERT: G 103 ASN cc_start: 0.9317 (m-40) cc_final: 0.9024 (m-40) REVERT: G 138 ASP cc_start: 0.8825 (t0) cc_final: 0.8600 (t0) REVERT: K 16 TYR cc_start: 0.8870 (m-80) cc_final: 0.8410 (m-80) REVERT: K 87 ARG cc_start: 0.8838 (ptp-110) cc_final: 0.8308 (ptp-170) REVERT: K 99 ARG cc_start: 0.9010 (ttm170) cc_final: 0.8527 (tpp80) REVERT: K 103 ASN cc_start: 0.9476 (m-40) cc_final: 0.9191 (m-40) REVERT: K 108 MET cc_start: 0.8721 (mtt) cc_final: 0.8367 (mtt) REVERT: K 117 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8723 (tp40) REVERT: K 119 GLN cc_start: 0.8370 (pm20) cc_final: 0.8100 (pm20) REVERT: K 136 GLN cc_start: 0.9603 (mt0) cc_final: 0.9235 (mp10) REVERT: K 143 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8425 (ptpp) REVERT: L 1 MET cc_start: 0.8812 (tpp) cc_final: 0.8081 (tpp) REVERT: L 9 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8870 (mtpp) REVERT: L 17 LYS cc_start: 0.9208 (mptt) cc_final: 0.8830 (mmtm) REVERT: L 18 GLU cc_start: 0.8462 (pp20) cc_final: 0.8041 (pp20) REVERT: L 32 TYR cc_start: 0.8706 (m-10) cc_final: 0.8117 (m-10) REVERT: L 45 ASP cc_start: 0.9281 (t70) cc_final: 0.9018 (t0) REVERT: L 80 ASP cc_start: 0.8770 (m-30) cc_final: 0.8519 (m-30) REVERT: L 81 GLU cc_start: 0.8452 (pp20) cc_final: 0.7766 (pp20) REVERT: L 90 ASP cc_start: 0.8895 (p0) cc_final: 0.8400 (p0) REVERT: L 92 ASP cc_start: 0.7503 (m-30) cc_final: 0.6328 (m-30) REVERT: L 120 GLU cc_start: 0.8847 (tp30) cc_final: 0.8624 (tp30) REVERT: M 68 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8529 (mtmt) REVERT: N 31 ASP cc_start: 0.8905 (m-30) cc_final: 0.8627 (m-30) REVERT: N 48 GLU cc_start: 0.8835 (tp30) cc_final: 0.8511 (tp30) REVERT: N 55 ASN cc_start: 0.9311 (m110) cc_final: 0.9013 (m-40) REVERT: N 67 ASN cc_start: 0.8557 (m110) cc_final: 0.8347 (m-40) REVERT: N 93 TRP cc_start: 0.8876 (m100) cc_final: 0.7389 (m100) REVERT: O 42 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8045 (mtp85) REVERT: O 101 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8404 (mm-30) REVERT: O 107 ASN cc_start: 0.9008 (t0) cc_final: 0.8651 (t0) REVERT: P 8 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7023 (tm-30) REVERT: P 51 LEU cc_start: 0.9418 (mt) cc_final: 0.9086 (mt) REVERT: P 98 GLU cc_start: 0.8636 (tp30) cc_final: 0.8004 (tp30) REVERT: P 126 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9102 (mmmt) REVERT: R 91 ASP cc_start: 0.7800 (p0) cc_final: 0.7412 (p0) REVERT: R 102 ASP cc_start: 0.8966 (t0) cc_final: 0.8516 (t0) REVERT: S 66 GLU cc_start: 0.8483 (pm20) cc_final: 0.8039 (pm20) REVERT: S 84 TYR cc_start: 0.8880 (t80) cc_final: 0.8540 (t80) REVERT: T 16 TYR cc_start: 0.9350 (m-80) cc_final: 0.9046 (m-80) REVERT: T 37 GLU cc_start: 0.8821 (mp0) cc_final: 0.8530 (mp0) REVERT: T 41 ASP cc_start: 0.9059 (m-30) cc_final: 0.8833 (m-30) REVERT: T 60 SER cc_start: 0.9407 (t) cc_final: 0.8867 (p) REVERT: T 97 GLN cc_start: 0.8524 (mm110) cc_final: 0.8259 (mm-40) REVERT: U 6 ASP cc_start: 0.8916 (t0) cc_final: 0.8145 (t0) REVERT: U 9 ASP cc_start: 0.8656 (m-30) cc_final: 0.8428 (m-30) REVERT: U 37 SER cc_start: 0.8914 (m) cc_final: 0.8577 (m) REVERT: U 62 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8582 (ttm170) REVERT: U 68 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8124 (mtm110) REVERT: U 69 THR cc_start: 0.8854 (m) cc_final: 0.8529 (m) REVERT: V 39 ASN cc_start: 0.9141 (t0) cc_final: 0.8322 (t0) REVERT: V 41 ILE cc_start: 0.9324 (pt) cc_final: 0.8942 (tp) REVERT: V 72 MET cc_start: 0.8527 (ttm) cc_final: 0.8249 (ttm) REVERT: W 10 LYS cc_start: 0.9248 (tptp) cc_final: 0.8882 (tppt) REVERT: W 43 ASP cc_start: 0.8109 (m-30) cc_final: 0.7533 (p0) REVERT: W 45 GLN cc_start: 0.8399 (mp10) cc_final: 0.7344 (mp10) REVERT: W 70 ASP cc_start: 0.8958 (t70) cc_final: 0.8744 (p0) REVERT: W 84 ASP cc_start: 0.8838 (t0) cc_final: 0.8493 (t0) REVERT: W 93 GLN cc_start: 0.9221 (mt0) cc_final: 0.8178 (mt0) REVERT: W 105 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8424 (mmmt) REVERT: W 126 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7809 (tm-30) REVERT: W 138 LEU cc_start: 0.9291 (mt) cc_final: 0.8587 (tt) REVERT: W 161 GLN cc_start: 0.8536 (mp10) cc_final: 0.7842 (mp-120) REVERT: W 173 ASP cc_start: 0.9302 (t0) cc_final: 0.8933 (t70) REVERT: W 175 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9244 (mp0) REVERT: W 183 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8121 (tp30) REVERT: X 19 GLN cc_start: 0.8371 (mp10) cc_final: 0.8132 (mp10) REVERT: X 32 LYS cc_start: 0.8366 (mttt) cc_final: 0.7321 (mttt) REVERT: X 35 GLU cc_start: 0.8090 (mp0) cc_final: 0.7321 (mp0) REVERT: X 76 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8565 (mttp) REVERT: Y 57 LYS cc_start: 0.9355 (tttt) cc_final: 0.9010 (ttmm) REVERT: Z 19 LYS cc_start: 0.9413 (mtmm) cc_final: 0.9175 (mtmm) REVERT: Z 21 LYS cc_start: 0.9496 (ttmm) cc_final: 0.8686 (tppt) REVERT: Z 24 GLU cc_start: 0.8804 (mp0) cc_final: 0.8521 (mp0) REVERT: Z 27 GLU cc_start: 0.8304 (tp30) cc_final: 0.8103 (tp30) REVERT: Z 29 LEU cc_start: 0.9422 (tp) cc_final: 0.9178 (tt) REVERT: Z 31 ASN cc_start: 0.9445 (m110) cc_final: 0.8956 (m110) REVERT: Z 36 MET cc_start: 0.9164 (mmm) cc_final: 0.8895 (mmt) REVERT: Z 47 LEU cc_start: 0.9307 (mm) cc_final: 0.8735 (mm) REVERT: Z 51 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7909 (mtm110) REVERT: Z 52 GLN cc_start: 0.9144 (mt0) cc_final: 0.8680 (mm-40) REVERT: a 7 THR cc_start: 0.8917 (m) cc_final: 0.8225 (p) REVERT: a 8 GLN cc_start: 0.8730 (tt0) cc_final: 0.8441 (tt0) REVERT: a 11 SER cc_start: 0.9255 (t) cc_final: 0.8651 (p) REVERT: a 33 GLN cc_start: 0.8587 (mt0) cc_final: 0.8218 (mt0) REVERT: b 44 LEU cc_start: 0.9423 (tt) cc_final: 0.9134 (pp) REVERT: c 16 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8820 (mm-30) REVERT: c 39 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7914 (ttpt) REVERT: c 50 PRO cc_start: 0.8562 (Cg_exo) cc_final: 0.7942 (Cg_endo) REVERT: d 8 PHE cc_start: 0.9017 (t80) cc_final: 0.8503 (t80) REVERT: d 9 GLN cc_start: 0.9058 (mm110) cc_final: 0.8792 (mm110) REVERT: f 6 SER cc_start: 0.9232 (t) cc_final: 0.8714 (t) REVERT: f 8 LYS cc_start: 0.9061 (mttt) cc_final: 0.8773 (mttp) REVERT: f 18 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8434 (ttm-80) REVERT: f 36 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8121 (tm-30) outliers start: 0 outliers final: 0 residues processed: 998 average time/residue: 0.9735 time to fit residues: 1620.3415 Evaluate side-chains 885 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 363 optimal weight: 0.6980 chunk 465 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 536 optimal weight: 0.2980 chunk 356 optimal weight: 1.9990 chunk 635 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN E 208 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN G 169 GLN J 32 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 50 GLN Q 79 ASN R 38 GLN R 94 ASN S 88 GLN U 27 ASN V 4 HIS ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 105356 Z= 0.166 Angle : 0.561 10.011 158464 Z= 0.288 Chirality : 0.033 0.278 20367 Planarity : 0.004 0.057 8077 Dihedral : 24.512 179.863 54712 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.25 (0.14), residues: 3463 helix: 0.73 (0.17), residues: 956 sheet: 0.06 (0.18), residues: 845 loop : -0.76 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 206 HIS 0.006 0.001 HIS a 52 PHE 0.030 0.002 PHE Z 34 TYR 0.021 0.002 TYR R 76 ARG 0.030 0.001 ARG R 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1051 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 3 11 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8451 (mtm110) REVERT: 3 18 HIS cc_start: 0.9040 (m90) cc_final: 0.8663 (m90) REVERT: C 20 ASP cc_start: 0.9083 (t0) cc_final: 0.8854 (t0) REVERT: C 30 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8202 (mm-30) REVERT: C 109 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8787 (tm-30) REVERT: C 115 ASP cc_start: 0.8506 (m-30) cc_final: 0.8040 (m-30) REVERT: C 124 ASP cc_start: 0.8730 (t0) cc_final: 0.8085 (t0) REVERT: C 146 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 215 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8893 (mttm) REVERT: C 250 TRP cc_start: 0.9358 (m-90) cc_final: 0.8717 (m-90) REVERT: D 54 TYR cc_start: 0.8275 (t80) cc_final: 0.7575 (t80) REVERT: D 127 MET cc_start: 0.8776 (mtt) cc_final: 0.8427 (mtt) REVERT: D 154 CYS cc_start: 0.7511 (t) cc_final: 0.7310 (t) REVERT: D 166 MET cc_start: 0.8108 (mtp) cc_final: 0.7516 (mtp) REVERT: D 202 ASN cc_start: 0.8891 (m-40) cc_final: 0.8507 (m-40) REVERT: D 210 SER cc_start: 0.8697 (t) cc_final: 0.8043 (t) REVERT: E 19 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8109 (tp30) REVERT: E 66 TYR cc_start: 0.8868 (p90) cc_final: 0.8442 (p90) REVERT: E 76 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8285 (mm110) REVERT: E 106 MET cc_start: 0.8946 (mmt) cc_final: 0.8673 (mmt) REVERT: E 158 ILE cc_start: 0.9412 (mp) cc_final: 0.8746 (mp) REVERT: E 192 ASP cc_start: 0.8411 (m-30) cc_final: 0.8103 (m-30) REVERT: E 208 ASN cc_start: 0.8858 (m-40) cc_final: 0.8650 (m110) REVERT: F 58 ASN cc_start: 0.9519 (m110) cc_final: 0.9205 (m110) REVERT: F 129 PHE cc_start: 0.7799 (m-80) cc_final: 0.7461 (m-80) REVERT: F 139 LEU cc_start: 0.9697 (mm) cc_final: 0.9335 (pp) REVERT: F 170 ASP cc_start: 0.7712 (m-30) cc_final: 0.7359 (m-30) REVERT: G 36 ASP cc_start: 0.9259 (m-30) cc_final: 0.8960 (t0) REVERT: G 103 ASN cc_start: 0.9271 (m-40) cc_final: 0.9016 (m-40) REVERT: G 138 ASP cc_start: 0.8779 (t0) cc_final: 0.8512 (t0) REVERT: G 154 ARG cc_start: 0.9168 (mmm-85) cc_final: 0.8923 (mtp85) REVERT: J 137 MET cc_start: 0.1874 (mtm) cc_final: 0.1665 (ttm) REVERT: K 16 TYR cc_start: 0.8854 (m-80) cc_final: 0.8487 (m-80) REVERT: K 87 ARG cc_start: 0.8842 (ptp-110) cc_final: 0.8417 (ptp-170) REVERT: K 99 ARG cc_start: 0.8914 (ttm170) cc_final: 0.8491 (tpp80) REVERT: K 103 ASN cc_start: 0.9424 (m-40) cc_final: 0.9137 (m-40) REVERT: K 117 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8562 (tp-100) REVERT: K 120 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9004 (mmtt) REVERT: K 136 GLN cc_start: 0.9559 (mt0) cc_final: 0.9252 (mp10) REVERT: K 143 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8443 (ptpp) REVERT: L 1 MET cc_start: 0.8746 (tpp) cc_final: 0.7925 (tpp) REVERT: L 9 LYS cc_start: 0.9269 (ttpp) cc_final: 0.8816 (mtpp) REVERT: L 17 LYS cc_start: 0.9233 (mptt) cc_final: 0.8869 (mmtm) REVERT: L 18 GLU cc_start: 0.8411 (pp20) cc_final: 0.7942 (pp20) REVERT: L 32 TYR cc_start: 0.8638 (m-10) cc_final: 0.8059 (m-10) REVERT: L 35 ILE cc_start: 0.9329 (mt) cc_final: 0.9108 (mm) REVERT: L 45 ASP cc_start: 0.9294 (t70) cc_final: 0.9041 (t0) REVERT: L 80 ASP cc_start: 0.8679 (m-30) cc_final: 0.8338 (m-30) REVERT: L 81 GLU cc_start: 0.8451 (pp20) cc_final: 0.7626 (pp20) REVERT: L 90 ASP cc_start: 0.9093 (p0) cc_final: 0.8470 (p0) REVERT: L 92 ASP cc_start: 0.7458 (m-30) cc_final: 0.6019 (m-30) REVERT: L 120 GLU cc_start: 0.8754 (tp30) cc_final: 0.8526 (tp30) REVERT: N 8 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8599 (ttpt) REVERT: N 31 ASP cc_start: 0.8864 (m-30) cc_final: 0.8628 (m-30) REVERT: N 43 THR cc_start: 0.9338 (p) cc_final: 0.9133 (p) REVERT: N 55 ASN cc_start: 0.9359 (m110) cc_final: 0.9070 (m-40) REVERT: N 63 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8317 (tttt) REVERT: N 67 ASN cc_start: 0.8890 (m110) cc_final: 0.8518 (m-40) REVERT: N 93 TRP cc_start: 0.8633 (m100) cc_final: 0.7233 (m100) REVERT: N 105 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7038 (mt-10) REVERT: N 110 ASP cc_start: 0.8825 (t70) cc_final: 0.8604 (t70) REVERT: N 132 VAL cc_start: 0.9316 (t) cc_final: 0.9078 (m) REVERT: O 69 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8591 (ttmm) REVERT: O 107 ASN cc_start: 0.8858 (t0) cc_final: 0.8560 (t0) REVERT: P 8 GLN cc_start: 0.7588 (tm-30) cc_final: 0.6731 (tm-30) REVERT: P 51 LEU cc_start: 0.9414 (mt) cc_final: 0.9117 (mt) REVERT: P 93 LYS cc_start: 0.9422 (ptpp) cc_final: 0.9164 (pttp) REVERT: P 98 GLU cc_start: 0.8671 (tp30) cc_final: 0.8063 (tp30) REVERT: P 126 LYS cc_start: 0.9363 (mmpt) cc_final: 0.9039 (mmmt) REVERT: Q 38 ARG cc_start: 0.8629 (ptt90) cc_final: 0.7807 (ptm-80) REVERT: Q 49 ARG cc_start: 0.8979 (mmm-85) cc_final: 0.8743 (mmm-85) REVERT: Q 99 LEU cc_start: 0.9425 (mt) cc_final: 0.9170 (mp) REVERT: R 3 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8210 (ttt90) REVERT: R 22 LYS cc_start: 0.9274 (mtpp) cc_final: 0.9035 (mttm) REVERT: R 24 TYR cc_start: 0.8887 (m-10) cc_final: 0.8332 (m-80) REVERT: R 91 ASP cc_start: 0.7882 (p0) cc_final: 0.7579 (p0) REVERT: R 102 ASP cc_start: 0.8876 (t0) cc_final: 0.8417 (t0) REVERT: S 66 GLU cc_start: 0.8539 (pm20) cc_final: 0.8011 (pm20) REVERT: T 16 TYR cc_start: 0.9269 (m-80) cc_final: 0.8998 (m-80) REVERT: T 37 GLU cc_start: 0.8804 (mp0) cc_final: 0.8549 (mp0) REVERT: T 41 ASP cc_start: 0.9056 (m-30) cc_final: 0.8819 (m-30) REVERT: T 60 SER cc_start: 0.9405 (t) cc_final: 0.8907 (p) REVERT: T 115 GLU cc_start: 0.8081 (tp30) cc_final: 0.7855 (tp30) REVERT: U 6 ASP cc_start: 0.8849 (t0) cc_final: 0.8024 (t0) REVERT: U 68 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8027 (mtm110) REVERT: U 69 THR cc_start: 0.8867 (m) cc_final: 0.8506 (m) REVERT: U 76 ARG cc_start: 0.8544 (mtt180) cc_final: 0.7731 (mtp180) REVERT: U 81 ARG cc_start: 0.8541 (mtt180) cc_final: 0.8232 (mtt180) REVERT: V 39 ASN cc_start: 0.9006 (t0) cc_final: 0.8207 (t0) REVERT: V 41 ILE cc_start: 0.9306 (pt) cc_final: 0.8966 (tp) REVERT: W 10 LYS cc_start: 0.9238 (tptp) cc_final: 0.8958 (tppt) REVERT: W 32 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7960 (mmmt) REVERT: W 43 ASP cc_start: 0.8045 (m-30) cc_final: 0.7408 (p0) REVERT: W 45 GLN cc_start: 0.8438 (mp10) cc_final: 0.7276 (mp10) REVERT: W 70 ASP cc_start: 0.8918 (t70) cc_final: 0.8693 (p0) REVERT: W 84 ASP cc_start: 0.8771 (t0) cc_final: 0.8479 (t0) REVERT: W 93 GLN cc_start: 0.9221 (mt0) cc_final: 0.8226 (mt0) REVERT: W 126 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7878 (tm-30) REVERT: W 161 GLN cc_start: 0.8473 (mp10) cc_final: 0.7784 (mp-120) REVERT: W 173 ASP cc_start: 0.9278 (t0) cc_final: 0.8882 (t70) REVERT: W 175 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9192 (mp0) REVERT: W 183 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8139 (tp30) REVERT: X 35 GLU cc_start: 0.8071 (mp0) cc_final: 0.7533 (mp0) REVERT: X 76 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8494 (mttp) REVERT: Y 16 LYS cc_start: 0.8058 (tppp) cc_final: 0.7563 (mmmt) REVERT: Y 57 LYS cc_start: 0.9295 (tttt) cc_final: 0.8996 (ttmm) REVERT: Z 21 LYS cc_start: 0.9503 (ttmm) cc_final: 0.8981 (tppt) REVERT: Z 27 GLU cc_start: 0.8223 (tp30) cc_final: 0.8013 (tp30) REVERT: Z 31 ASN cc_start: 0.9429 (m110) cc_final: 0.8882 (m110) REVERT: Z 47 LEU cc_start: 0.9351 (mm) cc_final: 0.9089 (mm) REVERT: Z 51 ARG cc_start: 0.8353 (mtm110) cc_final: 0.8068 (mtm110) REVERT: Z 52 GLN cc_start: 0.9081 (mt0) cc_final: 0.8843 (mt0) REVERT: Z 59 THR cc_start: 0.9006 (m) cc_final: 0.8618 (p) REVERT: a 7 THR cc_start: 0.8906 (m) cc_final: 0.8234 (p) REVERT: a 8 GLN cc_start: 0.8753 (tt0) cc_final: 0.8458 (tt0) REVERT: a 11 SER cc_start: 0.9202 (t) cc_final: 0.8446 (p) REVERT: a 21 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9209 (mm-30) REVERT: a 48 ASN cc_start: 0.9611 (t0) cc_final: 0.9370 (t0) REVERT: c 16 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8602 (mm-30) REVERT: c 39 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7771 (ttpt) REVERT: c 50 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.7850 (Cg_endo) REVERT: c 52 LYS cc_start: 0.8058 (tptp) cc_final: 0.7779 (mmmt) REVERT: d 8 PHE cc_start: 0.8909 (t80) cc_final: 0.8471 (t80) REVERT: d 9 GLN cc_start: 0.9149 (mm110) cc_final: 0.8817 (mm110) REVERT: e 30 ARG cc_start: 0.8372 (mmt180) cc_final: 0.8118 (mmm160) REVERT: f 6 SER cc_start: 0.9127 (t) cc_final: 0.8811 (t) REVERT: f 18 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8484 (ttm-80) REVERT: f 36 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7849 (tm-30) outliers start: 1 outliers final: 1 residues processed: 1051 average time/residue: 0.9966 time to fit residues: 1738.2436 Evaluate side-chains 905 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 904 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 403 optimal weight: 0.0270 chunk 432 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 7.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN F 25 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN K 103 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 50 GLN S 88 GLN U 27 ASN V 101 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN c 51 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 105356 Z= 0.345 Angle : 0.635 13.338 158464 Z= 0.324 Chirality : 0.037 0.279 20367 Planarity : 0.005 0.056 8077 Dihedral : 24.500 179.761 54712 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.39 (0.14), residues: 3463 helix: 0.60 (0.17), residues: 945 sheet: 0.01 (0.18), residues: 835 loop : -0.85 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 92 HIS 0.006 0.001 HIS W 86 PHE 0.035 0.002 PHE G 124 TYR 0.024 0.002 TYR R 32 ARG 0.014 0.001 ARG Q 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1002 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8815 (ttp-110) cc_final: 0.8557 (mtm110) REVERT: C 20 ASP cc_start: 0.9003 (t0) cc_final: 0.8754 (t0) REVERT: C 30 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 83 GLU cc_start: 0.8589 (pt0) cc_final: 0.8118 (pt0) REVERT: C 84 TYR cc_start: 0.9178 (t80) cc_final: 0.8915 (t80) REVERT: C 115 ASP cc_start: 0.8389 (m-30) cc_final: 0.7951 (m-30) REVERT: C 124 ASP cc_start: 0.8739 (t0) cc_final: 0.8110 (t0) REVERT: C 146 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 250 TRP cc_start: 0.9402 (m-90) cc_final: 0.8907 (m-90) REVERT: D 13 MET cc_start: 0.8102 (ttm) cc_final: 0.7896 (ttt) REVERT: D 54 TYR cc_start: 0.8420 (t80) cc_final: 0.7861 (t80) REVERT: D 99 GLN cc_start: 0.9103 (tt0) cc_final: 0.8486 (tt0) REVERT: D 154 CYS cc_start: 0.7576 (t) cc_final: 0.7302 (t) REVERT: D 172 ASN cc_start: 0.8999 (t0) cc_final: 0.8779 (t0) REVERT: D 202 ASN cc_start: 0.8860 (m-40) cc_final: 0.8406 (m-40) REVERT: D 210 SER cc_start: 0.8881 (t) cc_final: 0.8061 (m) REVERT: E 19 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8128 (tp30) REVERT: E 66 TYR cc_start: 0.8853 (p90) cc_final: 0.8561 (p90) REVERT: E 76 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8542 (mm-40) REVERT: E 106 MET cc_start: 0.8969 (mmt) cc_final: 0.8712 (mmt) REVERT: E 192 ASP cc_start: 0.8302 (m-30) cc_final: 0.8049 (m-30) REVERT: E 193 ASP cc_start: 0.7908 (m-30) cc_final: 0.7612 (m-30) REVERT: F 58 ASN cc_start: 0.9476 (m110) cc_final: 0.9182 (m110) REVERT: F 84 PHE cc_start: 0.8458 (m-10) cc_final: 0.8038 (m-80) REVERT: F 121 PHE cc_start: 0.8484 (t80) cc_final: 0.8196 (t80) REVERT: F 129 PHE cc_start: 0.7878 (m-80) cc_final: 0.7501 (m-80) REVERT: F 139 LEU cc_start: 0.9689 (mm) cc_final: 0.9331 (pp) REVERT: F 170 ASP cc_start: 0.7492 (m-30) cc_final: 0.7194 (m-30) REVERT: G 36 ASP cc_start: 0.9189 (m-30) cc_final: 0.8844 (t0) REVERT: G 138 ASP cc_start: 0.8829 (t0) cc_final: 0.8570 (t0) REVERT: G 154 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8926 (mtp85) REVERT: K 16 TYR cc_start: 0.8829 (m-80) cc_final: 0.8424 (m-80) REVERT: K 70 THR cc_start: 0.9490 (p) cc_final: 0.9109 (p) REVERT: K 71 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8553 (mtmm) REVERT: K 103 ASN cc_start: 0.9370 (m110) cc_final: 0.8950 (m110) REVERT: K 108 MET cc_start: 0.8685 (mtt) cc_final: 0.8300 (mtt) REVERT: K 117 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8765 (tp40) REVERT: K 120 LYS cc_start: 0.9346 (mmtt) cc_final: 0.9058 (mmtt) REVERT: K 136 GLN cc_start: 0.9558 (mt0) cc_final: 0.9210 (mp10) REVERT: K 141 GLU cc_start: 0.8334 (pm20) cc_final: 0.8126 (pm20) REVERT: K 143 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8430 (ptpp) REVERT: L 1 MET cc_start: 0.8773 (tpp) cc_final: 0.7963 (tpp) REVERT: L 6 SER cc_start: 0.8702 (m) cc_final: 0.8457 (m) REVERT: L 9 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8876 (mtpp) REVERT: L 18 GLU cc_start: 0.8516 (pp20) cc_final: 0.8023 (pp20) REVERT: L 32 TYR cc_start: 0.8653 (m-10) cc_final: 0.8018 (m-10) REVERT: L 45 ASP cc_start: 0.9262 (t70) cc_final: 0.9056 (t0) REVERT: L 53 LYS cc_start: 0.9167 (mptt) cc_final: 0.8962 (mmtt) REVERT: L 81 GLU cc_start: 0.8418 (pp20) cc_final: 0.7696 (pp20) REVERT: L 90 ASP cc_start: 0.9115 (p0) cc_final: 0.8485 (p0) REVERT: L 92 ASP cc_start: 0.7522 (m-30) cc_final: 0.6054 (m-30) REVERT: M 68 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8489 (mtmt) REVERT: M 135 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8785 (tm-30) REVERT: N 31 ASP cc_start: 0.8925 (m-30) cc_final: 0.8653 (m-30) REVERT: N 55 ASN cc_start: 0.9358 (m110) cc_final: 0.9098 (m-40) REVERT: N 67 ASN cc_start: 0.8932 (m110) cc_final: 0.8415 (m-40) REVERT: N 93 TRP cc_start: 0.8817 (m100) cc_final: 0.7270 (m100) REVERT: N 105 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7099 (mt-10) REVERT: O 27 SER cc_start: 0.9559 (t) cc_final: 0.9304 (t) REVERT: O 67 MET cc_start: 0.9054 (mtm) cc_final: 0.8808 (mtm) REVERT: O 69 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8681 (ttmm) REVERT: O 107 ASN cc_start: 0.8917 (t0) cc_final: 0.8574 (t0) REVERT: P 8 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7152 (tm-30) REVERT: P 51 LEU cc_start: 0.9423 (mt) cc_final: 0.9148 (mt) REVERT: P 98 GLU cc_start: 0.8637 (tp30) cc_final: 0.8058 (tp30) REVERT: P 126 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9063 (mmmt) REVERT: Q 97 TYR cc_start: 0.9048 (m-80) cc_final: 0.8786 (m-10) REVERT: R 24 TYR cc_start: 0.8709 (m-10) cc_final: 0.8311 (m-80) REVERT: R 32 TYR cc_start: 0.9157 (t80) cc_final: 0.8861 (t80) REVERT: R 91 ASP cc_start: 0.7684 (p0) cc_final: 0.7359 (p0) REVERT: R 102 ASP cc_start: 0.8959 (t0) cc_final: 0.8504 (t0) REVERT: S 66 GLU cc_start: 0.8641 (pm20) cc_final: 0.8084 (pm20) REVERT: T 16 TYR cc_start: 0.9316 (m-80) cc_final: 0.9027 (m-80) REVERT: T 37 GLU cc_start: 0.8849 (mp0) cc_final: 0.8588 (mp0) REVERT: T 41 ASP cc_start: 0.9049 (m-30) cc_final: 0.8820 (m-30) REVERT: T 60 SER cc_start: 0.9386 (t) cc_final: 0.8845 (p) REVERT: T 92 ILE cc_start: 0.9570 (mp) cc_final: 0.9366 (mm) REVERT: U 6 ASP cc_start: 0.8923 (t0) cc_final: 0.8074 (t0) REVERT: U 25 GLU cc_start: 0.8551 (mp0) cc_final: 0.8286 (mp0) REVERT: U 63 GLN cc_start: 0.8833 (mp-120) cc_final: 0.8515 (pm20) REVERT: U 68 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8094 (mtm110) REVERT: U 69 THR cc_start: 0.8816 (m) cc_final: 0.8521 (m) REVERT: U 76 ARG cc_start: 0.8534 (mtt180) cc_final: 0.7749 (mtp180) REVERT: V 39 ASN cc_start: 0.9028 (t0) cc_final: 0.8325 (t0) REVERT: V 41 ILE cc_start: 0.9342 (pt) cc_final: 0.9033 (tp) REVERT: V 72 MET cc_start: 0.8495 (ttm) cc_final: 0.8223 (ttm) REVERT: V 77 ASP cc_start: 0.9376 (p0) cc_final: 0.9159 (p0) REVERT: W 10 LYS cc_start: 0.9238 (tptp) cc_final: 0.8984 (tppt) REVERT: W 32 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7781 (mmmt) REVERT: W 45 GLN cc_start: 0.8432 (mp10) cc_final: 0.7985 (mp10) REVERT: W 67 LEU cc_start: 0.9564 (mm) cc_final: 0.9329 (mm) REVERT: W 70 ASP cc_start: 0.8969 (t70) cc_final: 0.8697 (p0) REVERT: W 84 ASP cc_start: 0.8794 (t0) cc_final: 0.8518 (t0) REVERT: W 93 GLN cc_start: 0.9246 (mt0) cc_final: 0.8312 (mt0) REVERT: W 126 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7819 (tm-30) REVERT: W 161 GLN cc_start: 0.8467 (mp10) cc_final: 0.7758 (mp-120) REVERT: W 173 ASP cc_start: 0.9314 (t0) cc_final: 0.9100 (t0) REVERT: W 183 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8235 (tp30) REVERT: X 35 GLU cc_start: 0.8069 (mp0) cc_final: 0.7327 (mp0) REVERT: Y 6 ASP cc_start: 0.9306 (m-30) cc_final: 0.9081 (m-30) REVERT: Y 28 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7597 (ptm160) REVERT: Y 57 LYS cc_start: 0.9334 (tttt) cc_final: 0.8990 (ttmm) REVERT: Z 20 ASP cc_start: 0.8990 (m-30) cc_final: 0.8577 (m-30) REVERT: Z 21 LYS cc_start: 0.9466 (ttmm) cc_final: 0.8712 (tppt) REVERT: Z 31 ASN cc_start: 0.9446 (m110) cc_final: 0.8990 (m110) REVERT: Z 47 LEU cc_start: 0.9271 (mm) cc_final: 0.8501 (mt) REVERT: Z 51 ARG cc_start: 0.8356 (mtm110) cc_final: 0.7451 (mtm-85) REVERT: Z 52 GLN cc_start: 0.9100 (mt0) cc_final: 0.8872 (mt0) REVERT: a 7 THR cc_start: 0.8918 (m) cc_final: 0.8238 (p) REVERT: a 8 GLN cc_start: 0.8714 (tt0) cc_final: 0.8454 (tt0) REVERT: a 11 SER cc_start: 0.9194 (t) cc_final: 0.8598 (p) REVERT: a 21 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9305 (mm-30) REVERT: b 44 LEU cc_start: 0.9418 (tt) cc_final: 0.9158 (pp) REVERT: c 16 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8694 (mm-30) REVERT: c 27 LYS cc_start: 0.8481 (tttm) cc_final: 0.8278 (tttt) REVERT: c 39 LYS cc_start: 0.8439 (ttpt) cc_final: 0.7906 (ttpt) REVERT: c 50 PRO cc_start: 0.8423 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: d 8 PHE cc_start: 0.8940 (t80) cc_final: 0.8429 (t80) REVERT: d 9 GLN cc_start: 0.9019 (mm110) cc_final: 0.8718 (mm110) REVERT: f 6 SER cc_start: 0.9110 (t) cc_final: 0.8819 (t) REVERT: f 8 LYS cc_start: 0.9335 (mttm) cc_final: 0.9086 (mttp) REVERT: f 18 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8520 (ttm-80) REVERT: f 36 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1002 average time/residue: 1.0310 time to fit residues: 1733.4040 Evaluate side-chains 888 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 888 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 7.9990 chunk 608 optimal weight: 4.9990 chunk 555 optimal weight: 0.6980 chunk 591 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 464 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 534 optimal weight: 2.9990 chunk 559 optimal weight: 3.9990 chunk 589 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN E 208 ASN F 25 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 79 ASN S 88 GLN U 27 ASN V 101 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 105356 Z= 0.234 Angle : 0.585 11.556 158464 Z= 0.300 Chirality : 0.034 0.260 20367 Planarity : 0.005 0.055 8077 Dihedral : 24.476 179.879 54712 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.32 (0.14), residues: 3463 helix: 0.69 (0.17), residues: 945 sheet: 0.03 (0.18), residues: 834 loop : -0.81 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 45 HIS 0.009 0.001 HIS W 86 PHE 0.025 0.002 PHE F 182 TYR 0.023 0.002 TYR R 32 ARG 0.013 0.001 ARG c 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8550 (mtm110) REVERT: C 20 ASP cc_start: 0.9061 (t0) cc_final: 0.8854 (t0) REVERT: C 30 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8098 (mm-30) REVERT: C 84 TYR cc_start: 0.9186 (t80) cc_final: 0.8922 (t80) REVERT: C 109 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 115 ASP cc_start: 0.8410 (m-30) cc_final: 0.7980 (m-30) REVERT: C 124 ASP cc_start: 0.8729 (t0) cc_final: 0.8098 (t0) REVERT: C 146 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 195 GLU cc_start: 0.8003 (pm20) cc_final: 0.7576 (pm20) REVERT: C 215 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8842 (mttm) REVERT: C 250 TRP cc_start: 0.9354 (m-90) cc_final: 0.8928 (m-90) REVERT: D 54 TYR cc_start: 0.8294 (t80) cc_final: 0.7737 (t80) REVERT: D 127 MET cc_start: 0.8824 (mtt) cc_final: 0.8493 (mtt) REVERT: D 154 CYS cc_start: 0.7505 (t) cc_final: 0.7236 (t) REVERT: D 172 ASN cc_start: 0.8986 (t0) cc_final: 0.8768 (t0) REVERT: D 202 ASN cc_start: 0.8883 (m-40) cc_final: 0.8487 (m110) REVERT: D 210 SER cc_start: 0.8880 (t) cc_final: 0.8041 (m) REVERT: E 19 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8120 (tp30) REVERT: E 66 TYR cc_start: 0.8852 (p90) cc_final: 0.8506 (p90) REVERT: E 76 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8238 (mm110) REVERT: E 106 MET cc_start: 0.8978 (mmt) cc_final: 0.8685 (mmt) REVERT: F 58 ASN cc_start: 0.9456 (m110) cc_final: 0.9153 (m110) REVERT: F 84 PHE cc_start: 0.8465 (m-10) cc_final: 0.8250 (m-80) REVERT: F 129 PHE cc_start: 0.7997 (m-80) cc_final: 0.7669 (m-80) REVERT: F 139 LEU cc_start: 0.9678 (mm) cc_final: 0.9320 (pp) REVERT: F 170 ASP cc_start: 0.7557 (m-30) cc_final: 0.7169 (m-30) REVERT: F 184 PHE cc_start: 0.7851 (m-80) cc_final: 0.7554 (m-80) REVERT: G 36 ASP cc_start: 0.9206 (m-30) cc_final: 0.8892 (t0) REVERT: G 138 ASP cc_start: 0.8816 (t0) cc_final: 0.8553 (t0) REVERT: K 13 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8612 (mmt-90) REVERT: K 16 TYR cc_start: 0.8791 (m-80) cc_final: 0.8435 (m-80) REVERT: K 67 ASP cc_start: 0.8571 (p0) cc_final: 0.7153 (p0) REVERT: K 71 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8510 (mtmm) REVERT: K 103 ASN cc_start: 0.9360 (m110) cc_final: 0.8991 (m-40) REVERT: K 108 MET cc_start: 0.8562 (mtt) cc_final: 0.8233 (mtt) REVERT: K 117 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8722 (tp40) REVERT: K 136 GLN cc_start: 0.9562 (mt0) cc_final: 0.9228 (mp10) REVERT: K 141 GLU cc_start: 0.8280 (pm20) cc_final: 0.8074 (pm20) REVERT: K 143 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8441 (ptpp) REVERT: L 1 MET cc_start: 0.8768 (tpp) cc_final: 0.7940 (tpp) REVERT: L 9 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8897 (mtpp) REVERT: L 18 GLU cc_start: 0.8453 (pp20) cc_final: 0.7944 (pp20) REVERT: L 32 TYR cc_start: 0.8689 (m-10) cc_final: 0.8061 (m-10) REVERT: L 35 ILE cc_start: 0.9331 (mt) cc_final: 0.9100 (mm) REVERT: L 53 LYS cc_start: 0.9180 (mptt) cc_final: 0.8980 (mmtt) REVERT: L 81 GLU cc_start: 0.8395 (pp20) cc_final: 0.7703 (pp20) REVERT: L 90 ASP cc_start: 0.9113 (p0) cc_final: 0.8474 (p0) REVERT: L 92 ASP cc_start: 0.7528 (m-30) cc_final: 0.6012 (m-30) REVERT: L 120 GLU cc_start: 0.8831 (tp30) cc_final: 0.8607 (tp30) REVERT: M 68 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8494 (mtmt) REVERT: N 31 ASP cc_start: 0.8887 (m-30) cc_final: 0.8650 (m-30) REVERT: N 55 ASN cc_start: 0.9353 (m110) cc_final: 0.9095 (m-40) REVERT: N 67 ASN cc_start: 0.8939 (m110) cc_final: 0.8386 (m-40) REVERT: N 93 TRP cc_start: 0.8772 (m100) cc_final: 0.7383 (m100) REVERT: N 132 VAL cc_start: 0.9336 (t) cc_final: 0.9090 (m) REVERT: O 107 ASN cc_start: 0.8846 (t0) cc_final: 0.8562 (t0) REVERT: P 8 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7137 (tm-30) REVERT: P 51 LEU cc_start: 0.9425 (mt) cc_final: 0.9151 (mt) REVERT: P 93 LYS cc_start: 0.9418 (ptpp) cc_final: 0.9085 (pttm) REVERT: P 98 GLU cc_start: 0.8629 (tp30) cc_final: 0.8051 (tp30) REVERT: P 126 LYS cc_start: 0.9399 (mmpt) cc_final: 0.9085 (mmmt) REVERT: Q 97 TYR cc_start: 0.8992 (m-80) cc_final: 0.8690 (m-10) REVERT: R 3 ARG cc_start: 0.8718 (ttt90) cc_final: 0.8268 (ttt90) REVERT: R 22 LYS cc_start: 0.9247 (mtpp) cc_final: 0.9046 (mttm) REVERT: R 24 TYR cc_start: 0.8748 (m-10) cc_final: 0.8208 (m-80) REVERT: R 32 TYR cc_start: 0.9039 (t80) cc_final: 0.8808 (t80) REVERT: R 91 ASP cc_start: 0.7789 (p0) cc_final: 0.7455 (p0) REVERT: R 102 ASP cc_start: 0.8923 (t0) cc_final: 0.8462 (t0) REVERT: S 66 GLU cc_start: 0.8648 (pm20) cc_final: 0.8110 (pm20) REVERT: T 37 GLU cc_start: 0.8841 (mp0) cc_final: 0.8560 (mp0) REVERT: T 41 ASP cc_start: 0.9033 (m-30) cc_final: 0.8741 (m-30) REVERT: T 60 SER cc_start: 0.9384 (t) cc_final: 0.8836 (p) REVERT: T 97 GLN cc_start: 0.9069 (mm110) cc_final: 0.8731 (mm-40) REVERT: T 115 GLU cc_start: 0.6767 (tp30) cc_final: 0.6476 (tp30) REVERT: U 6 ASP cc_start: 0.8875 (t0) cc_final: 0.8022 (t0) REVERT: U 25 GLU cc_start: 0.8508 (mp0) cc_final: 0.8294 (mp0) REVERT: U 63 GLN cc_start: 0.8859 (mp-120) cc_final: 0.8620 (pm20) REVERT: U 68 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8138 (mtm110) REVERT: U 76 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7678 (mtp180) REVERT: V 39 ASN cc_start: 0.8980 (t0) cc_final: 0.8260 (t0) REVERT: V 41 ILE cc_start: 0.9337 (pt) cc_final: 0.9023 (tp) REVERT: V 72 MET cc_start: 0.8437 (ttm) cc_final: 0.8199 (ttm) REVERT: V 77 ASP cc_start: 0.9355 (p0) cc_final: 0.9144 (p0) REVERT: W 10 LYS cc_start: 0.9279 (tptp) cc_final: 0.8953 (tppt) REVERT: W 45 GLN cc_start: 0.8361 (mp10) cc_final: 0.7939 (mp10) REVERT: W 67 LEU cc_start: 0.9570 (mm) cc_final: 0.9323 (mm) REVERT: W 70 ASP cc_start: 0.8979 (t70) cc_final: 0.8667 (p0) REVERT: W 84 ASP cc_start: 0.8813 (t0) cc_final: 0.8566 (t0) REVERT: W 93 GLN cc_start: 0.9114 (mt0) cc_final: 0.8147 (mt0) REVERT: W 161 GLN cc_start: 0.8437 (mp10) cc_final: 0.7734 (mp-120) REVERT: W 173 ASP cc_start: 0.9309 (t0) cc_final: 0.9092 (t0) REVERT: W 183 GLU cc_start: 0.8372 (tp30) cc_final: 0.8055 (tp30) REVERT: X 11 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7843 (ptp90) REVERT: X 35 GLU cc_start: 0.8109 (mp0) cc_final: 0.7527 (mp0) REVERT: Y 28 ARG cc_start: 0.8445 (ptm160) cc_final: 0.7710 (ptm160) REVERT: Y 37 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: Y 57 LYS cc_start: 0.9324 (tttt) cc_final: 0.9018 (ttmm) REVERT: Z 20 ASP cc_start: 0.9142 (m-30) cc_final: 0.8793 (m-30) REVERT: Z 21 LYS cc_start: 0.9523 (ttmm) cc_final: 0.8735 (tppt) REVERT: Z 24 GLU cc_start: 0.8961 (mp0) cc_final: 0.8578 (pm20) REVERT: Z 31 ASN cc_start: 0.9406 (m110) cc_final: 0.8897 (m110) REVERT: Z 47 LEU cc_start: 0.9293 (mm) cc_final: 0.8992 (mt) REVERT: Z 51 ARG cc_start: 0.8364 (mtm110) cc_final: 0.8101 (mtm110) REVERT: Z 52 GLN cc_start: 0.9067 (mt0) cc_final: 0.8836 (mt0) REVERT: a 7 THR cc_start: 0.8918 (m) cc_final: 0.8232 (p) REVERT: a 8 GLN cc_start: 0.8718 (tt0) cc_final: 0.8432 (tt0) REVERT: a 11 SER cc_start: 0.9213 (t) cc_final: 0.8538 (p) REVERT: a 21 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9159 (mm-30) REVERT: a 48 ASN cc_start: 0.9597 (t0) cc_final: 0.9375 (t0) REVERT: b 35 GLN cc_start: 0.8621 (pm20) cc_final: 0.8415 (pm20) REVERT: c 16 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8677 (mm-30) REVERT: c 39 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7906 (ttpt) REVERT: c 50 PRO cc_start: 0.8514 (Cg_exo) cc_final: 0.7838 (Cg_endo) REVERT: d 8 PHE cc_start: 0.8912 (t80) cc_final: 0.8395 (t80) REVERT: d 9 GLN cc_start: 0.9020 (mm110) cc_final: 0.8710 (mm110) REVERT: e 30 ARG cc_start: 0.8454 (mmt180) cc_final: 0.8210 (mmm160) REVERT: f 8 LYS cc_start: 0.9323 (mttm) cc_final: 0.9081 (mttp) REVERT: f 12 ASP cc_start: 0.9089 (p0) cc_final: 0.8420 (p0) REVERT: f 15 ARG cc_start: 0.7997 (mmp80) cc_final: 0.7493 (mmt-90) REVERT: f 18 ARG cc_start: 0.8960 (mtp85) cc_final: 0.8570 (ttm-80) REVERT: f 36 GLN cc_start: 0.8595 (tm-30) cc_final: 0.7849 (tm-30) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 1.0442 time to fit residues: 1749.9948 Evaluate side-chains 890 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 890 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 8.9990 chunk 625 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 5.9990 chunk 522 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 403 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN F 25 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN J 121 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN S 88 GLN U 27 ASN V 101 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 105356 Z= 0.295 Angle : 0.613 12.551 158464 Z= 0.313 Chirality : 0.036 0.269 20367 Planarity : 0.005 0.081 8077 Dihedral : 24.464 179.809 54712 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3463 helix: 0.57 (0.17), residues: 949 sheet: 0.03 (0.18), residues: 824 loop : -0.89 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.012 0.001 HIS W 86 PHE 0.032 0.002 PHE D 17 TYR 0.022 0.002 TYR R 32 ARG 0.011 0.001 ARG Q 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6926 Ramachandran restraints generated. 3463 Oldfield, 0 Emsley, 3463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 989 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 11 ARG cc_start: 0.8814 (ttp-110) cc_final: 0.8552 (mtm110) REVERT: C 20 ASP cc_start: 0.9065 (t0) cc_final: 0.8862 (t0) REVERT: C 30 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8217 (mm-30) REVERT: C 84 TYR cc_start: 0.9240 (t80) cc_final: 0.8989 (t80) REVERT: C 104 TYR cc_start: 0.8539 (m-80) cc_final: 0.8167 (m-80) REVERT: C 109 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 115 ASP cc_start: 0.8395 (m-30) cc_final: 0.7966 (m-30) REVERT: C 124 ASP cc_start: 0.8735 (t0) cc_final: 0.8100 (t0) REVERT: C 146 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 195 GLU cc_start: 0.7909 (pm20) cc_final: 0.7500 (pm20) REVERT: C 250 TRP cc_start: 0.9390 (m-90) cc_final: 0.9026 (m-90) REVERT: D 18 ASP cc_start: 0.9076 (t0) cc_final: 0.8811 (t0) REVERT: D 54 TYR cc_start: 0.8301 (t80) cc_final: 0.7727 (t80) REVERT: D 127 MET cc_start: 0.8850 (mtt) cc_final: 0.8524 (mtt) REVERT: D 154 CYS cc_start: 0.7496 (t) cc_final: 0.7212 (t) REVERT: D 166 MET cc_start: 0.7986 (mtp) cc_final: 0.7424 (mtp) REVERT: D 172 ASN cc_start: 0.9005 (t0) cc_final: 0.8804 (t0) REVERT: D 210 SER cc_start: 0.8884 (t) cc_final: 0.8058 (m) REVERT: E 19 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8132 (tp30) REVERT: E 66 TYR cc_start: 0.8835 (p90) cc_final: 0.8593 (p90) REVERT: E 76 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8512 (mm-40) REVERT: E 106 MET cc_start: 0.8992 (mmt) cc_final: 0.8694 (mmt) REVERT: F 12 LYS cc_start: 0.9358 (tppt) cc_final: 0.9149 (tppt) REVERT: F 58 ASN cc_start: 0.9446 (m110) cc_final: 0.9140 (m110) REVERT: F 121 PHE cc_start: 0.8468 (t80) cc_final: 0.8143 (t80) REVERT: F 129 PHE cc_start: 0.8072 (m-80) cc_final: 0.7651 (m-80) REVERT: F 139 LEU cc_start: 0.9687 (mm) cc_final: 0.9316 (pp) REVERT: F 170 ASP cc_start: 0.7567 (m-30) cc_final: 0.7249 (m-30) REVERT: F 184 PHE cc_start: 0.7918 (m-80) cc_final: 0.7531 (m-80) REVERT: G 7 GLN cc_start: 0.8246 (tp40) cc_final: 0.7924 (tp40) REVERT: G 36 ASP cc_start: 0.9281 (m-30) cc_final: 0.8905 (t0) REVERT: G 138 ASP cc_start: 0.8832 (t0) cc_final: 0.8578 (t0) REVERT: K 16 TYR cc_start: 0.8843 (m-80) cc_final: 0.8484 (m-80) REVERT: K 71 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8535 (mtmm) REVERT: K 102 GLU cc_start: 0.9155 (pm20) cc_final: 0.8917 (pm20) REVERT: K 103 ASN cc_start: 0.9356 (m110) cc_final: 0.8983 (m110) REVERT: K 108 MET cc_start: 0.8663 (mtt) cc_final: 0.8288 (mtt) REVERT: K 117 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8777 (tp40) REVERT: K 120 LYS cc_start: 0.9421 (mmtt) cc_final: 0.9108 (mmtt) REVERT: K 136 GLN cc_start: 0.9556 (mt0) cc_final: 0.9211 (mp10) REVERT: K 141 GLU cc_start: 0.8308 (pm20) cc_final: 0.8092 (pm20) REVERT: K 143 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8439 (ptpp) REVERT: L 1 MET cc_start: 0.8766 (tpp) cc_final: 0.7936 (tpp) REVERT: L 9 LYS cc_start: 0.9272 (ttpp) cc_final: 0.8997 (mtpp) REVERT: L 18 GLU cc_start: 0.8487 (pp20) cc_final: 0.7988 (pp20) REVERT: L 32 TYR cc_start: 0.8711 (m-10) cc_final: 0.8076 (m-10) REVERT: L 35 ILE cc_start: 0.9332 (mt) cc_final: 0.9105 (mm) REVERT: L 81 GLU cc_start: 0.8379 (pp20) cc_final: 0.7954 (pp20) REVERT: L 90 ASP cc_start: 0.9122 (p0) cc_final: 0.8481 (p0) REVERT: L 92 ASP cc_start: 0.7559 (m-30) cc_final: 0.6049 (m-30) REVERT: L 120 GLU cc_start: 0.8834 (tp30) cc_final: 0.8623 (tp30) REVERT: M 15 GLU cc_start: 0.8189 (pm20) cc_final: 0.7882 (pm20) REVERT: M 60 ARG cc_start: 0.8490 (pmt170) cc_final: 0.8260 (pmt170) REVERT: M 68 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8394 (mtmt) REVERT: N 31 ASP cc_start: 0.8923 (m-30) cc_final: 0.8680 (m-30) REVERT: N 55 ASN cc_start: 0.9354 (m110) cc_final: 0.9070 (m-40) REVERT: N 67 ASN cc_start: 0.8791 (m110) cc_final: 0.8525 (m-40) REVERT: N 83 MET cc_start: 0.8396 (mmp) cc_final: 0.8008 (mmp) REVERT: N 93 TRP cc_start: 0.8806 (m100) cc_final: 0.7449 (m100) REVERT: N 105 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7018 (mt-10) REVERT: N 106 LEU cc_start: 0.8996 (tp) cc_final: 0.8771 (tp) REVERT: N 132 VAL cc_start: 0.9441 (t) cc_final: 0.9139 (m) REVERT: O 27 SER cc_start: 0.9552 (t) cc_final: 0.9278 (t) REVERT: O 82 GLU cc_start: 0.8254 (mp0) cc_final: 0.7968 (mp0) REVERT: O 101 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8459 (mm-30) REVERT: O 107 ASN cc_start: 0.8908 (t0) cc_final: 0.8496 (t0) REVERT: P 8 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7145 (tm-30) REVERT: P 51 LEU cc_start: 0.9445 (mt) cc_final: 0.9184 (mt) REVERT: P 93 LYS cc_start: 0.9436 (ptpp) cc_final: 0.9123 (pttm) REVERT: P 98 GLU cc_start: 0.8643 (tp30) cc_final: 0.8071 (tp30) REVERT: P 126 LYS cc_start: 0.9413 (mmpt) cc_final: 0.9102 (mmmt) REVERT: Q 97 TYR cc_start: 0.9017 (m-80) cc_final: 0.8718 (m-10) REVERT: R 24 TYR cc_start: 0.8746 (m-10) cc_final: 0.8238 (m-80) REVERT: R 91 ASP cc_start: 0.7686 (p0) cc_final: 0.7400 (p0) REVERT: R 102 ASP cc_start: 0.8947 (t0) cc_final: 0.8488 (t0) REVERT: S 66 GLU cc_start: 0.8690 (pm20) cc_final: 0.8126 (pm20) REVERT: T 37 GLU cc_start: 0.8845 (mp0) cc_final: 0.8575 (mp0) REVERT: T 41 ASP cc_start: 0.9035 (m-30) cc_final: 0.8756 (m-30) REVERT: T 60 SER cc_start: 0.9392 (t) cc_final: 0.8837 (p) REVERT: T 97 GLN cc_start: 0.9049 (mm110) cc_final: 0.8702 (mm-40) REVERT: U 6 ASP cc_start: 0.8897 (t0) cc_final: 0.8038 (t0) REVERT: U 63 GLN cc_start: 0.8892 (mp-120) cc_final: 0.8472 (pm20) REVERT: U 68 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8109 (mtm110) REVERT: U 76 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7698 (mtp180) REVERT: V 39 ASN cc_start: 0.9002 (t0) cc_final: 0.8288 (t0) REVERT: V 41 ILE cc_start: 0.9348 (pt) cc_final: 0.8770 (tp) REVERT: V 72 MET cc_start: 0.8497 (ttm) cc_final: 0.8235 (ttm) REVERT: V 77 ASP cc_start: 0.9385 (p0) cc_final: 0.9171 (p0) REVERT: W 10 LYS cc_start: 0.9271 (tptp) cc_final: 0.9003 (tppt) REVERT: W 32 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8040 (mmmt) REVERT: W 43 ASP cc_start: 0.8120 (m-30) cc_final: 0.7898 (m-30) REVERT: W 45 GLN cc_start: 0.8394 (mp10) cc_final: 0.7849 (mp10) REVERT: W 67 LEU cc_start: 0.9565 (mm) cc_final: 0.9322 (mm) REVERT: W 70 ASP cc_start: 0.9017 (t70) cc_final: 0.8685 (p0) REVERT: W 84 ASP cc_start: 0.8835 (t0) cc_final: 0.8551 (t0) REVERT: W 93 GLN cc_start: 0.9210 (mt0) cc_final: 0.8321 (mt0) REVERT: W 126 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7627 (tm-30) REVERT: W 161 GLN cc_start: 0.8445 (mp10) cc_final: 0.7733 (mp-120) REVERT: W 173 ASP cc_start: 0.9302 (t0) cc_final: 0.9050 (t0) REVERT: X 11 ARG cc_start: 0.8188 (ptp90) cc_final: 0.7750 (ptp90) REVERT: X 35 GLU cc_start: 0.8033 (mp0) cc_final: 0.7297 (mp0) REVERT: Y 16 LYS cc_start: 0.8494 (tppp) cc_final: 0.8025 (mmmt) REVERT: Y 28 ARG cc_start: 0.8456 (ptm160) cc_final: 0.7516 (ptm160) REVERT: Y 37 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: Y 57 LYS cc_start: 0.9324 (tttt) cc_final: 0.9031 (ttmm) REVERT: Z 20 ASP cc_start: 0.9165 (m-30) cc_final: 0.8882 (m-30) REVERT: Z 21 LYS cc_start: 0.9513 (ttmm) cc_final: 0.8982 (tppt) REVERT: Z 31 ASN cc_start: 0.9417 (m110) cc_final: 0.9079 (m110) REVERT: Z 47 LEU cc_start: 0.9280 (mm) cc_final: 0.8498 (mt) REVERT: Z 51 ARG cc_start: 0.8371 (mtm110) cc_final: 0.7697 (mtm110) REVERT: Z 52 GLN cc_start: 0.9077 (mt0) cc_final: 0.8845 (mt0) REVERT: a 7 THR cc_start: 0.8924 (m) cc_final: 0.8236 (p) REVERT: a 8 GLN cc_start: 0.8695 (tt0) cc_final: 0.8406 (tt0) REVERT: a 11 SER cc_start: 0.9163 (t) cc_final: 0.8596 (p) REVERT: a 21 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9197 (mm-30) REVERT: b 35 GLN cc_start: 0.8625 (pm20) cc_final: 0.8391 (pm20) REVERT: c 16 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8773 (mm-30) REVERT: c 29 ARG cc_start: 0.9039 (ptt90) cc_final: 0.8816 (ptt-90) REVERT: c 30 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8148 (mmp80) REVERT: c 39 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7967 (ttpt) REVERT: c 50 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: c 51 HIS cc_start: 0.8129 (m-70) cc_final: 0.7813 (m170) REVERT: c 53 GLU cc_start: 0.8979 (pp20) cc_final: 0.8749 (pm20) REVERT: d 8 PHE cc_start: 0.8902 (t80) cc_final: 0.8371 (t80) REVERT: d 9 GLN cc_start: 0.8985 (mm110) cc_final: 0.8685 (mm110) REVERT: e 13 ARG cc_start: 0.7359 (mmt90) cc_final: 0.7072 (mmt90) REVERT: e 30 ARG cc_start: 0.8504 (mmt180) cc_final: 0.8244 (mmm160) REVERT: f 8 LYS cc_start: 0.9330 (mttm) cc_final: 0.9041 (mttp) REVERT: f 18 ARG cc_start: 0.8987 (mtp85) cc_final: 0.8612 (ttm-80) REVERT: f 36 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7848 (tm-30) outliers start: 0 outliers final: 0 residues processed: 989 average time/residue: 1.0302 time to fit residues: 1708.4619 Evaluate side-chains 886 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 886 time to evaluate : 3.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 0.9990 chunk 556 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 482 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 523 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 537 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 13 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN F 25 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 79 ASN S 88 GLN U 27 ASN V 101 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 ASN a 42 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.053708 restraints weight = 368280.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055389 restraints weight = 129741.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.056364 restraints weight = 69562.860| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 105356 Z= 0.297 Angle : 0.614 13.113 158464 Z= 0.314 Chirality : 0.036 0.266 20367 Planarity : 0.005 0.056 8077 Dihedral : 24.465 179.951 54712 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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 (0.14), residues: 3463 helix: 0.60 (0.17), residues: 948 sheet: -0.02 (0.18), residues: 811 loop : -0.91 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 92 HIS 0.010 0.001 HIS W 86 PHE 0.025 0.002 PHE R 57 TYR 0.029 0.002 TYR T 16 ARG 0.011 0.001 ARG O 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24442.79 seconds wall clock time: 430 minutes 46.76 seconds (25846.76 seconds total)