Starting phenix.real_space_refine on Sat Mar 23 06:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/03_2024/7boi_12244_updated.pdb" } resolution = 2.98 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= 0.005 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 1 6.06 5 P 1081 5.49 5 Mg 72 5.21 5 S 51 5.16 5 C 18274 2.51 5 N 6688 2.21 5 O 9803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35970 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 23172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 23172 Classifications: {'RNA': 1078} Modifications used: {'rna2p': 1, 'rna2p_pur': 79, 'rna2p_pyr': 52, 'rna3p': 7, 'rna3p_pur': 542, 'rna3p_pyr': 397} Link IDs: {'rna2p': 131, 'rna3p': 946} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "W" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2456 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Unusual residues: {' MG': 70} Classifications: {'undetermined': 70} Link IDs: {None: 69} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35454 SG CYS W 297 103.267 175.784 111.924 1.00138.41 S ATOM 35500 SG CYS W 302 100.646 176.420 109.591 1.00139.90 S ATOM 35559 SG CYS W 310 104.236 175.553 107.507 1.00143.63 S Time building chain proxies: 18.10, per 1000 atoms: 0.50 Number of scatterers: 35970 At special positions: 0 Unit cell: (137.795, 218.085, 147.56, 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 1 29.99 S 51 16.00 P 1081 15.00 Mg 72 11.99 O 9803 8.00 N 6688 7.00 C 18274 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: 20.90 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN W 401 " pdb="ZN ZN W 401 " - pdb=" ND1 HIS W 304 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 297 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 310 " pdb="ZN ZN W 401 " - pdb=" SG CYS W 302 " Number of angles added : 3 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 15 sheets defined 35.3% alpha, 17.6% beta 371 base pairs and 591 stacking pairs defined. Time for finding SS restraints: 22.28 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.573A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 removed outlier: 3.650A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 164 removed outlier: 4.647A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.711A pdb=" N GLU D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 32 removed outlier: 4.036A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.766A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 removed outlier: 3.942A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.092A pdb=" N VAL O 29 " --> pdb=" O THR O 25 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.328A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 3.908A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.596A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 29 through 32 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 40 Processing helix chain 'T' and resid 45 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'U' and resid 12 through 25 Processing helix chain 'U' and resid 28 through 34 Processing helix chain 'U' and resid 41 through 64 removed outlier: 3.781A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 150 removed outlier: 3.507A pdb=" N ASP W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 183 removed outlier: 3.945A pdb=" N GLU W 175 " --> pdb=" O ALA W 171 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN W 176 " --> pdb=" O PHE W 172 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE W 179 " --> pdb=" O GLU W 175 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR W 180 " --> pdb=" O GLN W 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG W 181 " --> pdb=" O MET W 177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE W 183 " --> pdb=" O ILE W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 205 Processing helix chain 'W' and resid 220 through 228 Processing helix chain 'W' and resid 280 through 286 Processing helix chain 'W' and resid 288 through 293 removed outlier: 3.741A pdb=" N HIS W 291 " --> pdb=" O VAL W 288 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP W 292 " --> pdb=" O GLU W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 317 Processing helix chain 'W' and resid 323 through 340 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.002A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.488A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 92 through 98 Processing sheet with id= D, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.914A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.981A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.903A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.656A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN K 81 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA K 21 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU K 83 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE K 23 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET K 85 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA K 25 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS K 87 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG K 106 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL K 84 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N VAL K 86 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N ILE K 110 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.761A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 2 through 9 Processing sheet with id= J, first strand: chain 'P' and resid 37 through 39 Processing sheet with id= K, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.495A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.488A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'W' and resid 78 through 81 removed outlier: 6.672A pdb=" N ASP W 53 " --> pdb=" O ILE W 45 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG W 47 " --> pdb=" O HIS W 51 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS W 51 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY W 95 " --> pdb=" O ASN W 65 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL W 80 " --> pdb=" O GLU W 98 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'W' and resid 254 through 257 removed outlier: 5.661A pdb=" N ARG W 208 " --> pdb=" O ASP W 263 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE W 265 " --> pdb=" O ARG W 208 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER W 210 " --> pdb=" O ILE W 265 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN W 125 " --> pdb=" O ILE W 211 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA W 213 " --> pdb=" O GLN W 125 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL W 127 " --> pdb=" O ALA W 213 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU W 154 " --> pdb=" O ILE W 126 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE W 128 " --> pdb=" O GLU W 154 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE W 156 " --> pdb=" O ILE W 128 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N SER W 130 " --> pdb=" O ILE W 156 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL W 158 " --> pdb=" O SER W 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'W' and resid 106 through 111 removed outlier: 3.686A pdb=" N ALA W 120 " --> pdb=" O LEU W 107 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG W 109 " --> pdb=" O PRO W 118 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP W 111 " --> pdb=" O VAL W 116 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL W 116 " --> pdb=" O ASP W 111 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 912 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 371 basepair parallelities 591 stacking parallelities Total time for adding SS restraints: 30.47 Time building geometry restraints manager: 21.79 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: 6295 1.33 - 1.45: 15483 1.45 - 1.58: 14844 1.58 - 1.70: 2159 1.70 - 1.82: 85 Bond restraints: 38866 Sorted by residual: bond pdb=" C1' GNP W 402 " pdb=" C2' GNP W 402 " ideal model delta sigma weight residual 1.273 1.525 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C3' GNP W 402 " pdb=" C4' GNP W 402 " ideal model delta sigma weight residual 1.285 1.534 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C2 4OC A1402 " pdb=" N3 4OC A1402 " ideal model delta sigma weight residual 1.507 1.343 0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.308 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C1' GNP W 402 " pdb=" O4' GNP W 402 " ideal model delta sigma weight residual 1.564 1.411 0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 38861 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.87: 3527 103.87 - 111.99: 23074 111.99 - 120.11: 16919 120.11 - 128.23: 12602 128.23 - 136.35: 1732 Bond angle restraints: 57854 Sorted by residual: angle pdb=" N LEU R 67 " pdb=" CA LEU R 67 " pdb=" C LEU R 67 " ideal model delta sigma weight residual 112.90 104.38 8.52 1.31e+00 5.83e-01 4.23e+01 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 112.61 129.32 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" C3' G7M A 527 " pdb=" C2' G7M A 527 " pdb=" C1' G7M A 527 " ideal model delta sigma weight residual 101.30 95.75 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N6 MA6 A1519 " pdb=" C6 MA6 A1519 " pdb=" N1 MA6 A1519 " ideal model delta sigma weight residual 104.44 120.42 -15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 104.44 120.41 -15.97 3.00e+00 1.11e-01 2.83e+01 ... (remaining 57849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 21863 35.75 - 71.49: 2658 71.49 - 107.24: 279 107.24 - 142.98: 7 142.98 - 178.73: 5 Dihedral angle restraints: 24812 sinusoidal: 20175 harmonic: 4637 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 55.23 144.77 1 1.50e+01 4.44e-03 7.75e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 61.60 138.40 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" O4' C A1400 " pdb=" C1' C A1400 " pdb=" N1 C A1400 " pdb=" C2 C A1400 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 24809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 6796 0.086 - 0.172: 438 0.172 - 0.258: 68 0.258 - 0.343: 5 0.343 - 0.429: 3 Chirality restraints: 7310 Sorted by residual: chirality pdb=" CA GLU F 33 " pdb=" N GLU F 33 " pdb=" C GLU F 33 " pdb=" CB GLU F 33 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA LYS Q 19 " pdb=" N LYS Q 19 " pdb=" C LYS Q 19 " pdb=" CB LYS Q 19 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 7307 not shown) Planarity restraints: 3337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP W 402 " -0.458 2.00e-02 2.50e+03 6.17e-01 8.57e+03 pdb=" C2' GNP W 402 " 0.627 2.00e-02 2.50e+03 pdb=" C3' GNP W 402 " 0.175 2.00e-02 2.50e+03 pdb=" C4' GNP W 402 " -0.209 2.00e-02 2.50e+03 pdb=" C5' GNP W 402 " 0.921 2.00e-02 2.50e+03 pdb=" N9 GNP W 402 " -0.057 2.00e-02 2.50e+03 pdb=" O2' GNP W 402 " 0.678 2.00e-02 2.50e+03 pdb=" O3' GNP W 402 " -0.968 2.00e-02 2.50e+03 pdb=" O4' GNP W 402 " -0.709 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.051 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C4' 5MC A1407 " 0.433 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.590 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.610 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.187 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.956 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.233 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.871 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.037 2.00e-02 2.50e+03 5.65e-01 7.18e+03 pdb=" C4' 2MG A1516 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.593 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.568 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.919 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.236 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.849 2.00e-02 2.50e+03 ... (remaining 3334 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 379 2.53 - 3.12: 26700 3.12 - 3.71: 74228 3.71 - 4.31: 101976 4.31 - 4.90: 135912 Nonbonded interactions: 339195 Sorted by model distance: nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1667 " model vdw 1.934 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1627 " model vdw 1.962 2.170 nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1642 " model vdw 1.963 2.170 nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1622 " model vdw 1.964 2.170 nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1667 " model vdw 1.976 2.170 ... (remaining 339190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.630 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 132.300 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 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 : 0.008 0.252 38866 Z= 0.487 Angle : 0.759 16.708 57854 Z= 0.475 Chirality : 0.047 0.429 7310 Planarity : 0.019 0.617 3337 Dihedral : 22.918 178.731 21820 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 16.58 % Favored : 83.42 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.20), residues: 1588 helix: -0.78 (0.20), residues: 588 sheet: -1.49 (0.29), residues: 279 loop : -1.17 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS K 118 PHE 0.016 0.001 PHE W 172 TYR 0.012 0.001 TYR L 38 ARG 0.004 0.000 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 2.077 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: E 13 GLU cc_start: 0.8236 (mp0) cc_final: 0.7880 (mp0) REVERT: E 23 LYS cc_start: 0.9087 (ttpt) cc_final: 0.7887 (mmtt) REVERT: E 31 PHE cc_start: 0.8973 (m-80) cc_final: 0.8715 (m-80) REVERT: E 50 TYR cc_start: 0.9078 (t80) cc_final: 0.8757 (t80) REVERT: E 61 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8885 (tp40) REVERT: F 59 TYR cc_start: 0.8137 (m-80) cc_final: 0.7783 (m-80) REVERT: H 50 LYS cc_start: 0.8551 (pttp) cc_final: 0.8321 (pttp) REVERT: H 52 GLU cc_start: 0.8506 (mp0) cc_final: 0.7571 (mp0) REVERT: H 59 LEU cc_start: 0.9661 (tp) cc_final: 0.9323 (tp) REVERT: H 61 LEU cc_start: 0.9620 (mp) cc_final: 0.9085 (mt) REVERT: H 64 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8664 (mtpt) REVERT: H 73 GLU cc_start: 0.8473 (pp20) cc_final: 0.8166 (pp20) REVERT: H 111 MET cc_start: 0.8605 (ptp) cc_final: 0.8396 (ptp) REVERT: K 64 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8537 (tm-30) REVERT: K 68 GLU cc_start: 0.9273 (mp0) cc_final: 0.8748 (pm20) REVERT: K 83 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8243 (mp0) REVERT: K 87 LYS cc_start: 0.9346 (ptmm) cc_final: 0.8998 (pttm) REVERT: K 126 LYS cc_start: 0.9108 (tppt) cc_final: 0.8870 (tppt) REVERT: L 47 SER cc_start: 0.8796 (m) cc_final: 0.8420 (p) REVERT: L 73 ASN cc_start: 0.9067 (p0) cc_final: 0.8729 (p0) REVERT: O 64 ARG cc_start: 0.8350 (tpm170) cc_final: 0.8051 (tpp-160) REVERT: O 68 ASP cc_start: 0.8174 (m-30) cc_final: 0.7879 (m-30) REVERT: O 80 GLN cc_start: 0.8525 (pp30) cc_final: 0.8052 (pp30) REVERT: P 12 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8966 (ttpp) REVERT: P 18 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7880 (mm-40) REVERT: P 44 SER cc_start: 0.8221 (p) cc_final: 0.6359 (t) REVERT: P 76 LYS cc_start: 0.9020 (tttt) cc_final: 0.8423 (tttt) REVERT: Q 8 LEU cc_start: 0.9518 (mt) cc_final: 0.8777 (mp) REVERT: Q 16 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8713 (mtmt) REVERT: Q 61 ILE cc_start: 0.9613 (pt) cc_final: 0.9362 (pp) REVERT: R 18 VAL cc_start: 0.8579 (t) cc_final: 0.8369 (p) REVERT: R 22 ASP cc_start: 0.7950 (t0) cc_final: 0.7513 (t70) REVERT: R 32 TYR cc_start: 0.9239 (m-80) cc_final: 0.8980 (m-80) REVERT: R 51 TYR cc_start: 0.9092 (m-80) cc_final: 0.8788 (m-10) REVERT: U 20 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8987 (tmmt) REVERT: U 31 GLU cc_start: 0.8641 (tp30) cc_final: 0.8173 (tp30) REVERT: U 39 GLU cc_start: 0.8385 (tt0) cc_final: 0.8123 (tt0) REVERT: U 58 LYS cc_start: 0.9442 (mtpt) cc_final: 0.9191 (tmmt) REVERT: W 152 GLN cc_start: 0.9411 (mm110) cc_final: 0.9131 (mp10) REVERT: W 180 TYR cc_start: 0.9270 (m-80) cc_final: 0.9037 (m-80) REVERT: W 282 GLN cc_start: 0.9317 (mt0) cc_final: 0.8819 (mt0) outliers start: 0 outliers final: 3 residues processed: 504 average time/residue: 1.6900 time to fit residues: 994.6120 Evaluate side-chains 373 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 370 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain T residue 39 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 67 GLN H 118 GLN K 38 GLN Q 9 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 338 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 38866 Z= 0.337 Angle : 0.641 20.624 57854 Z= 0.331 Chirality : 0.036 0.373 7310 Planarity : 0.005 0.130 3337 Dihedral : 23.287 174.851 18655 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.80 % Allowed : 24.12 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.21), residues: 1588 helix: 0.18 (0.21), residues: 596 sheet: -1.19 (0.29), residues: 291 loop : -0.85 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 42 HIS 0.005 0.001 HIS L 77 PHE 0.024 0.002 PHE F 80 TYR 0.018 0.002 TYR W 299 ARG 0.012 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 404 time to evaluate : 2.002 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: D 196 ASN cc_start: 0.9148 (m110) cc_final: 0.8811 (m-40) REVERT: E 14 LYS cc_start: 0.8955 (tppp) cc_final: 0.7606 (ttmt) REVERT: E 20 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8768 (ttp80) REVERT: E 23 LYS cc_start: 0.9118 (ttpt) cc_final: 0.7962 (mmtt) REVERT: E 31 PHE cc_start: 0.8929 (m-80) cc_final: 0.8695 (m-80) REVERT: E 50 TYR cc_start: 0.9109 (t80) cc_final: 0.8762 (t80) REVERT: E 60 ILE cc_start: 0.9499 (pp) cc_final: 0.9169 (mt) REVERT: E 61 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8778 (tp-100) REVERT: E 69 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8359 (mtm-85) REVERT: E 101 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: E 124 LEU cc_start: 0.9540 (mt) cc_final: 0.9301 (mm) REVERT: E 156 LYS cc_start: 0.9483 (ptpp) cc_final: 0.9260 (ptpp) REVERT: F 72 ASP cc_start: 0.8804 (m-30) cc_final: 0.8525 (m-30) REVERT: H 59 LEU cc_start: 0.9659 (tp) cc_final: 0.9259 (tp) REVERT: H 61 LEU cc_start: 0.9508 (mp) cc_final: 0.9183 (mt) REVERT: K 64 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8737 (tm-30) REVERT: K 68 GLU cc_start: 0.9243 (mp0) cc_final: 0.8775 (mp0) REVERT: K 83 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8304 (mp0) REVERT: K 87 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9039 (pttm) REVERT: K 126 LYS cc_start: 0.9075 (tppt) cc_final: 0.8859 (tppt) REVERT: L 47 SER cc_start: 0.8910 (m) cc_final: 0.8510 (p) REVERT: L 62 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8036 (mm-30) REVERT: L 73 ASN cc_start: 0.9102 (p0) cc_final: 0.8793 (p0) REVERT: O 64 ARG cc_start: 0.8297 (tpm170) cc_final: 0.8071 (tpp-160) REVERT: O 68 ASP cc_start: 0.8164 (m-30) cc_final: 0.7934 (m-30) REVERT: O 80 GLN cc_start: 0.8392 (pp30) cc_final: 0.7993 (tm-30) REVERT: P 18 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7915 (mm-40) REVERT: P 76 LYS cc_start: 0.8987 (tttt) cc_final: 0.8649 (tttt) REVERT: Q 16 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8724 (mtmt) REVERT: Q 27 ARG cc_start: 0.8826 (ptt90) cc_final: 0.8563 (ptt90) REVERT: Q 60 GLU cc_start: 0.7616 (tp30) cc_final: 0.7386 (tp30) REVERT: R 16 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8726 (mp0) REVERT: R 18 VAL cc_start: 0.8588 (t) cc_final: 0.8377 (p) REVERT: R 33 ILE cc_start: 0.9558 (pt) cc_final: 0.9226 (pp) REVERT: R 51 TYR cc_start: 0.9046 (m-80) cc_final: 0.8804 (m-10) REVERT: U 31 GLU cc_start: 0.8602 (tp30) cc_final: 0.8201 (tp30) REVERT: U 39 GLU cc_start: 0.8379 (tt0) cc_final: 0.8164 (tt0) REVERT: U 56 HIS cc_start: 0.9352 (t70) cc_final: 0.9130 (t70) REVERT: U 58 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9202 (tmmt) REVERT: W 152 GLN cc_start: 0.9408 (mm110) cc_final: 0.9116 (mp10) REVERT: W 282 GLN cc_start: 0.9376 (mt0) cc_final: 0.9003 (mt0) REVERT: W 310 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7149 (t) outliers start: 91 outliers final: 45 residues processed: 447 average time/residue: 1.5418 time to fit residues: 820.1163 Evaluate side-chains 421 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 374 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 80 LYS Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 310 CYS Chi-restraints excluded: chain W residue 345 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 118 GLN K 38 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN W 62 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 38866 Z= 0.323 Angle : 0.622 16.786 57854 Z= 0.322 Chirality : 0.036 0.365 7310 Planarity : 0.005 0.132 3337 Dihedral : 23.214 175.047 18653 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 7.32 % Allowed : 26.06 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1588 helix: 0.51 (0.22), residues: 596 sheet: -1.04 (0.30), residues: 290 loop : -0.72 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.005 0.001 HIS K 22 PHE 0.014 0.001 PHE F 80 TYR 0.017 0.002 TYR W 299 ARG 0.009 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 389 time to evaluate : 2.442 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: D 198 HIS cc_start: 0.8890 (p90) cc_final: 0.8678 (p-80) REVERT: E 14 LYS cc_start: 0.8766 (tppp) cc_final: 0.8565 (ttmt) REVERT: E 20 ARG cc_start: 0.9048 (ttp-170) cc_final: 0.8454 (ttp80) REVERT: E 23 LYS cc_start: 0.9133 (ttpt) cc_final: 0.7975 (mmtt) REVERT: E 31 PHE cc_start: 0.8937 (m-80) cc_final: 0.8353 (m-80) REVERT: E 50 TYR cc_start: 0.9106 (t80) cc_final: 0.8784 (t80) REVERT: E 60 ILE cc_start: 0.9498 (pp) cc_final: 0.9173 (mt) REVERT: E 61 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8804 (tp-100) REVERT: E 116 GLU cc_start: 0.8148 (pp20) cc_final: 0.7755 (pm20) REVERT: F 1 MET cc_start: 0.8697 (ptp) cc_final: 0.8068 (tmm) REVERT: F 72 ASP cc_start: 0.8670 (m-30) cc_final: 0.8463 (m-30) REVERT: H 42 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8042 (tm-30) REVERT: H 43 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8345 (mm-30) REVERT: H 59 LEU cc_start: 0.9624 (tp) cc_final: 0.9331 (tp) REVERT: K 14 LYS cc_start: 0.8722 (tmmm) cc_final: 0.7648 (mptt) REVERT: K 64 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8703 (tm-30) REVERT: K 68 GLU cc_start: 0.9203 (mp0) cc_final: 0.8738 (mp0) REVERT: K 83 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8295 (mp0) REVERT: K 87 LYS cc_start: 0.9357 (ptmm) cc_final: 0.8987 (pttm) REVERT: K 126 LYS cc_start: 0.9055 (tppt) cc_final: 0.8853 (tppt) REVERT: L 47 SER cc_start: 0.8946 (m) cc_final: 0.8562 (p) REVERT: O 10 LYS cc_start: 0.9083 (tppt) cc_final: 0.8804 (ttmm) REVERT: O 64 ARG cc_start: 0.8312 (tpm170) cc_final: 0.8073 (tpp-160) REVERT: O 68 ASP cc_start: 0.8146 (m-30) cc_final: 0.7917 (m-30) REVERT: O 80 GLN cc_start: 0.8391 (pp30) cc_final: 0.8015 (tm-30) REVERT: P 18 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7868 (mm-40) REVERT: P 76 LYS cc_start: 0.8953 (tttt) cc_final: 0.8597 (tttt) REVERT: Q 8 LEU cc_start: 0.9465 (mp) cc_final: 0.9163 (mp) REVERT: Q 16 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8730 (mtmt) REVERT: Q 80 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8033 (tm-30) REVERT: R 33 ILE cc_start: 0.9558 (pt) cc_final: 0.9234 (pp) REVERT: R 51 TYR cc_start: 0.9046 (m-80) cc_final: 0.8805 (m-10) REVERT: U 31 GLU cc_start: 0.8565 (tp30) cc_final: 0.8118 (tp30) REVERT: U 39 GLU cc_start: 0.8354 (tt0) cc_final: 0.8101 (tt0) REVERT: U 56 HIS cc_start: 0.9344 (t70) cc_final: 0.9118 (t70) REVERT: U 58 LYS cc_start: 0.9423 (mtpt) cc_final: 0.9194 (tmmt) REVERT: W 152 GLN cc_start: 0.9400 (mm110) cc_final: 0.9111 (mp10) REVERT: W 282 GLN cc_start: 0.9347 (mt0) cc_final: 0.9036 (mt0) REVERT: W 310 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7223 (t) REVERT: W 340 LYS cc_start: 0.8513 (ptpt) cc_final: 0.7980 (tptp) outliers start: 98 outliers final: 51 residues processed: 434 average time/residue: 1.5745 time to fit residues: 810.5039 Evaluate side-chains 423 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 371 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 310 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 239 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 118 GLN K 38 GLN Q 9 GLN T 52 ASN T 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38866 Z= 0.184 Angle : 0.581 16.342 57854 Z= 0.300 Chirality : 0.032 0.343 7310 Planarity : 0.005 0.126 3337 Dihedral : 23.145 177.911 18653 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.05 % Allowed : 28.38 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1588 helix: 0.87 (0.22), residues: 581 sheet: -0.89 (0.30), residues: 287 loop : -0.50 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.005 0.001 HIS R 74 PHE 0.032 0.001 PHE W 172 TYR 0.014 0.001 TYR W 329 ARG 0.011 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 405 time to evaluate : 2.220 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: E 23 LYS cc_start: 0.9125 (ttpt) cc_final: 0.7944 (mmtt) REVERT: E 31 PHE cc_start: 0.8918 (m-80) cc_final: 0.8420 (m-10) REVERT: E 50 TYR cc_start: 0.9091 (t80) cc_final: 0.8754 (t80) REVERT: E 60 ILE cc_start: 0.9498 (pp) cc_final: 0.9170 (mt) REVERT: E 61 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8715 (tp40) REVERT: E 111 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: E 116 GLU cc_start: 0.8237 (pp20) cc_final: 0.7727 (pp20) REVERT: E 140 THR cc_start: 0.9620 (p) cc_final: 0.9408 (t) REVERT: F 1 MET cc_start: 0.8472 (ptp) cc_final: 0.8026 (tmm) REVERT: F 54 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8545 (tt) REVERT: F 72 ASP cc_start: 0.8560 (m-30) cc_final: 0.8256 (m-30) REVERT: K 64 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8600 (tm-30) REVERT: K 68 GLU cc_start: 0.9148 (mp0) cc_final: 0.8600 (mp0) REVERT: K 83 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: K 87 LYS cc_start: 0.9352 (ptmm) cc_final: 0.8955 (pttm) REVERT: L 25 GLU cc_start: 0.8353 (mp0) cc_final: 0.8112 (mp0) REVERT: L 47 SER cc_start: 0.8948 (m) cc_final: 0.8560 (p) REVERT: O 64 ARG cc_start: 0.8227 (tpm170) cc_final: 0.7937 (tpp-160) REVERT: O 80 GLN cc_start: 0.8393 (pp30) cc_final: 0.8009 (tm-30) REVERT: P 76 LYS cc_start: 0.8912 (tttt) cc_final: 0.8400 (tttt) REVERT: Q 16 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8767 (mtmt) REVERT: R 33 ILE cc_start: 0.9519 (pt) cc_final: 0.9194 (pp) REVERT: R 47 THR cc_start: 0.9541 (m) cc_final: 0.9212 (t) REVERT: R 51 TYR cc_start: 0.9033 (m-80) cc_final: 0.8781 (m-10) REVERT: U 4 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8522 (pp) REVERT: U 31 GLU cc_start: 0.8493 (tp30) cc_final: 0.7755 (tp30) REVERT: U 56 HIS cc_start: 0.9336 (t70) cc_final: 0.9113 (t70) REVERT: U 58 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9189 (tmmt) REVERT: W 152 GLN cc_start: 0.9367 (mm110) cc_final: 0.9085 (mp10) REVERT: W 282 GLN cc_start: 0.9254 (mt0) cc_final: 0.9023 (mt0) outliers start: 81 outliers final: 43 residues processed: 441 average time/residue: 1.5358 time to fit residues: 807.9280 Evaluate side-chains 428 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 381 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 227 optimal weight: 0.0050 chunk 63 optimal weight: 10.0000 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 196 ASN D 198 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN Q 9 GLN T 61 GLN ** W 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38866 Z= 0.216 Angle : 0.593 16.356 57854 Z= 0.305 Chirality : 0.032 0.318 7310 Planarity : 0.005 0.127 3337 Dihedral : 23.098 177.867 18653 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.80 % Allowed : 29.35 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.21), residues: 1588 helix: 0.94 (0.22), residues: 581 sheet: -0.74 (0.30), residues: 287 loop : -0.34 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 60 HIS 0.005 0.001 HIS R 74 PHE 0.013 0.001 PHE U 12 TYR 0.018 0.002 TYR F 59 ARG 0.009 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 389 time to evaluate : 2.182 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: D 196 ASN cc_start: 0.9021 (m110) cc_final: 0.8659 (m-40) REVERT: E 23 LYS cc_start: 0.9168 (ttpt) cc_final: 0.7996 (mmtt) REVERT: E 50 TYR cc_start: 0.9105 (t80) cc_final: 0.8757 (t80) REVERT: E 61 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8901 (tp40) REVERT: E 116 GLU cc_start: 0.8271 (pp20) cc_final: 0.7914 (pp20) REVERT: F 54 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8663 (tt) REVERT: F 72 ASP cc_start: 0.8539 (m-30) cc_final: 0.8256 (m-30) REVERT: H 42 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 43 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8256 (mm-30) REVERT: H 76 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: H 118 GLN cc_start: 0.8846 (tt0) cc_final: 0.8452 (tm-30) REVERT: K 14 LYS cc_start: 0.8699 (tmmm) cc_final: 0.7634 (mptt) REVERT: K 64 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8576 (tm-30) REVERT: K 68 GLU cc_start: 0.9141 (mp0) cc_final: 0.8576 (mp0) REVERT: K 83 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: K 87 LYS cc_start: 0.9354 (ptmm) cc_final: 0.8963 (pttm) REVERT: L 47 SER cc_start: 0.8966 (m) cc_final: 0.8598 (p) REVERT: O 10 LYS cc_start: 0.9069 (tppt) cc_final: 0.8595 (ttmm) REVERT: O 11 ILE cc_start: 0.9646 (mm) cc_final: 0.9293 (mm) REVERT: O 64 ARG cc_start: 0.8258 (tpm170) cc_final: 0.8012 (tpp-160) REVERT: P 76 LYS cc_start: 0.8895 (tttt) cc_final: 0.8259 (tttt) REVERT: R 16 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8874 (mp0) REVERT: R 33 ILE cc_start: 0.9519 (pt) cc_final: 0.9192 (pp) REVERT: R 47 THR cc_start: 0.9537 (m) cc_final: 0.9185 (t) REVERT: R 51 TYR cc_start: 0.9039 (m-80) cc_final: 0.8692 (m-10) REVERT: U 4 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8621 (pp) REVERT: U 31 GLU cc_start: 0.8184 (tp30) cc_final: 0.7887 (tp30) REVERT: U 56 HIS cc_start: 0.9330 (t70) cc_final: 0.9112 (t70) REVERT: U 59 LYS cc_start: 0.9223 (mmtt) cc_final: 0.9005 (mmmm) REVERT: W 152 GLN cc_start: 0.9355 (mm110) cc_final: 0.9057 (mp10) REVERT: W 310 CYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7102 (t) outliers start: 91 outliers final: 59 residues processed: 431 average time/residue: 1.5652 time to fit residues: 801.4127 Evaluate side-chains 429 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 365 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 250 THR Chi-restraints excluded: chain W residue 310 CYS Chi-restraints excluded: chain W residue 345 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 198 HIS E 146 ASN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Q 9 GLN R 74 HIS ** W 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 38866 Z= 0.336 Angle : 0.644 16.459 57854 Z= 0.332 Chirality : 0.036 0.309 7310 Planarity : 0.005 0.131 3337 Dihedral : 23.108 176.212 18653 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.02 % Allowed : 31.44 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.21), residues: 1588 helix: 0.84 (0.22), residues: 581 sheet: -0.84 (0.29), residues: 304 loop : -0.37 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 60 HIS 0.006 0.001 HIS R 74 PHE 0.024 0.002 PHE W 172 TYR 0.015 0.002 TYR D 51 ARG 0.014 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 373 time to evaluate : 2.181 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: E 23 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8064 (mmtt) REVERT: E 50 TYR cc_start: 0.9140 (t80) cc_final: 0.8821 (t80) REVERT: E 61 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8848 (tp40) REVERT: E 68 ARG cc_start: 0.8876 (mmt-90) cc_final: 0.8649 (mmt-90) REVERT: F 54 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8599 (tt) REVERT: F 70 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8411 (m) REVERT: H 76 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: H 118 GLN cc_start: 0.8869 (tt0) cc_final: 0.8513 (tm-30) REVERT: K 14 LYS cc_start: 0.8696 (tmmm) cc_final: 0.7613 (mptp) REVERT: K 64 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8570 (tm-30) REVERT: K 68 GLU cc_start: 0.9153 (mp0) cc_final: 0.8587 (mp0) REVERT: K 83 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: K 87 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9013 (pttm) REVERT: L 47 SER cc_start: 0.8940 (m) cc_final: 0.8624 (p) REVERT: P 25 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8823 (mtm110) REVERT: P 76 LYS cc_start: 0.9046 (tttt) cc_final: 0.8555 (tttt) REVERT: R 33 ILE cc_start: 0.9539 (pt) cc_final: 0.9216 (pp) REVERT: R 47 THR cc_start: 0.9559 (m) cc_final: 0.9208 (t) REVERT: R 51 TYR cc_start: 0.9079 (m-80) cc_final: 0.8819 (m-10) REVERT: T 28 MET cc_start: 0.8892 (ttp) cc_final: 0.8574 (ttm) REVERT: U 31 GLU cc_start: 0.8054 (tp30) cc_final: 0.7444 (tp30) REVERT: U 59 LYS cc_start: 0.9218 (mmtt) cc_final: 0.9007 (mmmm) REVERT: W 152 GLN cc_start: 0.9362 (mm110) cc_final: 0.9063 (mp10) REVERT: W 298 LYS cc_start: 0.8675 (pptt) cc_final: 0.8389 (pptt) REVERT: W 310 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7255 (t) outliers start: 94 outliers final: 60 residues processed: 418 average time/residue: 1.5643 time to fit residues: 777.7201 Evaluate side-chains 425 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 359 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 250 THR Chi-restraints excluded: chain W residue 310 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 252 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 198 HIS F 63 ASN H 21 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** W 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38866 Z= 0.167 Angle : 0.606 16.241 57854 Z= 0.309 Chirality : 0.032 0.301 7310 Planarity : 0.005 0.124 3337 Dihedral : 23.072 178.707 18653 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.60 % Allowed : 33.91 % Favored : 60.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.21), residues: 1588 helix: 0.99 (0.22), residues: 568 sheet: -0.59 (0.30), residues: 291 loop : -0.24 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 170 HIS 0.004 0.001 HIS L 77 PHE 0.026 0.001 PHE U 37 TYR 0.019 0.001 TYR D 51 ARG 0.010 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 385 time to evaluate : 2.244 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: E 23 LYS cc_start: 0.9076 (ttpt) cc_final: 0.7983 (mmtt) REVERT: E 50 TYR cc_start: 0.9137 (t80) cc_final: 0.8782 (t80) REVERT: E 61 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8771 (tp40) REVERT: F 5 GLU cc_start: 0.8461 (tp30) cc_final: 0.8235 (tp30) REVERT: F 25 TYR cc_start: 0.8750 (m-80) cc_final: 0.8509 (m-80) REVERT: F 54 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8675 (tt) REVERT: H 42 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7860 (tm-30) REVERT: H 76 GLN cc_start: 0.8438 (pp30) cc_final: 0.8086 (pp30) REVERT: H 118 GLN cc_start: 0.8825 (tt0) cc_final: 0.8526 (tm-30) REVERT: K 14 LYS cc_start: 0.8768 (tmmm) cc_final: 0.7713 (mptp) REVERT: K 64 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8552 (tm-30) REVERT: K 68 GLU cc_start: 0.9116 (mp0) cc_final: 0.8583 (mp0) REVERT: K 87 LYS cc_start: 0.9343 (ptmm) cc_final: 0.8953 (pttm) REVERT: K 110 ILE cc_start: 0.9197 (mt) cc_final: 0.8947 (mm) REVERT: L 25 GLU cc_start: 0.8262 (mp0) cc_final: 0.8060 (mp0) REVERT: L 47 SER cc_start: 0.8940 (m) cc_final: 0.8606 (p) REVERT: P 48 GLU cc_start: 0.7820 (pt0) cc_final: 0.7540 (tt0) REVERT: P 76 LYS cc_start: 0.9026 (tttt) cc_final: 0.8471 (tttt) REVERT: R 33 ILE cc_start: 0.9505 (pt) cc_final: 0.9184 (pp) REVERT: R 47 THR cc_start: 0.9524 (m) cc_final: 0.9137 (t) REVERT: R 51 TYR cc_start: 0.9019 (m-80) cc_final: 0.8694 (m-10) REVERT: U 4 ILE cc_start: 0.8670 (tp) cc_final: 0.8316 (pp) REVERT: U 31 GLU cc_start: 0.8033 (tp30) cc_final: 0.7418 (tp30) REVERT: U 56 HIS cc_start: 0.9320 (t70) cc_final: 0.9117 (t70) REVERT: U 59 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8999 (mmmm) REVERT: W 152 GLN cc_start: 0.9324 (mm110) cc_final: 0.9031 (mp10) REVERT: W 299 TYR cc_start: 0.2157 (OUTLIER) cc_final: -0.0320 (m-80) outliers start: 75 outliers final: 43 residues processed: 421 average time/residue: 1.5382 time to fit residues: 773.5038 Evaluate side-chains 413 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 368 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Chi-restraints excluded: chain W residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN O 62 GLN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 38866 Z= 0.366 Angle : 0.674 16.466 57854 Z= 0.346 Chirality : 0.037 0.296 7310 Planarity : 0.005 0.130 3337 Dihedral : 23.076 176.426 18653 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.97 % Allowed : 34.88 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.21), residues: 1588 helix: 0.77 (0.22), residues: 577 sheet: -0.78 (0.29), residues: 314 loop : -0.23 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 60 HIS 0.005 0.001 HIS R 74 PHE 0.028 0.002 PHE W 172 TYR 0.019 0.002 TYR D 51 ARG 0.016 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 377 time to evaluate : 2.238 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: D 103 TYR cc_start: 0.9347 (t80) cc_final: 0.8962 (t80) REVERT: E 23 LYS cc_start: 0.9132 (ttpt) cc_final: 0.7965 (mmtt) REVERT: E 50 TYR cc_start: 0.9137 (t80) cc_final: 0.8798 (t80) REVERT: E 61 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8825 (tp40) REVERT: F 54 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8696 (tt) REVERT: H 42 GLU cc_start: 0.8227 (tm-30) cc_final: 0.8026 (tm-30) REVERT: H 76 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8117 (pp30) REVERT: H 118 GLN cc_start: 0.8868 (tt0) cc_final: 0.8595 (tm-30) REVERT: K 14 LYS cc_start: 0.8742 (tmmm) cc_final: 0.7744 (mptp) REVERT: K 64 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8581 (tm-30) REVERT: K 68 GLU cc_start: 0.9133 (mp0) cc_final: 0.8595 (mp0) REVERT: K 87 LYS cc_start: 0.9381 (ptmm) cc_final: 0.9009 (pttm) REVERT: L 47 SER cc_start: 0.8873 (m) cc_final: 0.8612 (p) REVERT: P 25 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8813 (mtm110) REVERT: P 76 LYS cc_start: 0.9032 (tttt) cc_final: 0.8639 (tttt) REVERT: R 24 LYS cc_start: 0.9391 (mtmp) cc_final: 0.9148 (mtmm) REVERT: R 33 ILE cc_start: 0.9541 (pt) cc_final: 0.9218 (pp) REVERT: R 47 THR cc_start: 0.9570 (m) cc_final: 0.9210 (t) REVERT: R 51 TYR cc_start: 0.9076 (m-80) cc_final: 0.8822 (m-10) REVERT: T 28 MET cc_start: 0.8938 (ttp) cc_final: 0.8638 (ttm) REVERT: U 4 ILE cc_start: 0.8763 (tp) cc_final: 0.8405 (pp) REVERT: U 59 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8997 (mmmm) REVERT: W 152 GLN cc_start: 0.9346 (mm110) cc_final: 0.9045 (mp10) REVERT: W 299 TYR cc_start: 0.2536 (OUTLIER) cc_final: 0.0170 (m-80) outliers start: 80 outliers final: 51 residues processed: 415 average time/residue: 1.5409 time to fit residues: 760.6502 Evaluate side-chains 416 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 361 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 299 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 196 ASN D 198 HIS H 21 ASN H 76 GLN K 38 GLN O 62 GLN ** W 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38866 Z= 0.160 Angle : 0.633 16.254 57854 Z= 0.323 Chirality : 0.032 0.293 7310 Planarity : 0.005 0.123 3337 Dihedral : 23.036 178.935 18653 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.48 % Allowed : 36.37 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.21), residues: 1588 helix: 0.95 (0.22), residues: 561 sheet: -0.61 (0.29), residues: 303 loop : -0.30 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 170 HIS 0.005 0.001 HIS L 77 PHE 0.024 0.001 PHE U 12 TYR 0.025 0.001 TYR D 51 ARG 0.013 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 389 time to evaluate : 2.356 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: D 103 TYR cc_start: 0.9296 (t80) cc_final: 0.8942 (t80) REVERT: E 23 LYS cc_start: 0.9050 (ttpt) cc_final: 0.7964 (mmtt) REVERT: E 31 PHE cc_start: 0.8892 (m-10) cc_final: 0.7970 (m-10) REVERT: E 33 PHE cc_start: 0.9305 (m-80) cc_final: 0.8976 (m-80) REVERT: E 50 TYR cc_start: 0.9145 (t80) cc_final: 0.8746 (t80) REVERT: E 68 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8755 (mmt-90) REVERT: F 5 GLU cc_start: 0.8833 (tp30) cc_final: 0.8432 (tp30) REVERT: F 9 MET cc_start: 0.8374 (ptp) cc_final: 0.7981 (mtm) REVERT: F 25 TYR cc_start: 0.8680 (m-80) cc_final: 0.8414 (m-80) REVERT: F 54 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8770 (tt) REVERT: F 59 TYR cc_start: 0.8322 (m-80) cc_final: 0.7939 (m-80) REVERT: F 90 MET cc_start: 0.8664 (ttp) cc_final: 0.8416 (mtp) REVERT: H 42 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7832 (tm-30) REVERT: H 43 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8163 (mm-30) REVERT: H 76 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8091 (pp30) REVERT: H 118 GLN cc_start: 0.8839 (tt0) cc_final: 0.8533 (tm-30) REVERT: K 14 LYS cc_start: 0.8763 (tmmm) cc_final: 0.7783 (mptt) REVERT: K 15 GLN cc_start: 0.9215 (mm110) cc_final: 0.8941 (mm-40) REVERT: K 64 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8524 (tm-30) REVERT: K 68 GLU cc_start: 0.9072 (mp0) cc_final: 0.8618 (mp0) REVERT: K 87 LYS cc_start: 0.9331 (ptmm) cc_final: 0.8925 (pttm) REVERT: L 25 GLU cc_start: 0.8296 (mp0) cc_final: 0.8069 (mp0) REVERT: L 47 SER cc_start: 0.8888 (m) cc_final: 0.8536 (p) REVERT: P 53 ASP cc_start: 0.8460 (t0) cc_final: 0.8027 (t0) REVERT: P 76 LYS cc_start: 0.8992 (tttt) cc_final: 0.8556 (tttt) REVERT: Q 80 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7484 (tm-30) REVERT: R 33 ILE cc_start: 0.9491 (pt) cc_final: 0.9172 (pp) REVERT: R 47 THR cc_start: 0.9535 (m) cc_final: 0.9153 (t) REVERT: R 51 TYR cc_start: 0.9007 (m-80) cc_final: 0.8629 (m-10) REVERT: U 20 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8737 (ttpp) REVERT: U 24 GLU cc_start: 0.8976 (pm20) cc_final: 0.8546 (pm20) REVERT: U 25 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9173 (tppt) REVERT: U 56 HIS cc_start: 0.9282 (t70) cc_final: 0.9081 (t70) REVERT: W 152 GLN cc_start: 0.9314 (mm110) cc_final: 0.9004 (mp10) REVERT: W 282 GLN cc_start: 0.9223 (mt0) cc_final: 0.8924 (mt0) outliers start: 60 outliers final: 41 residues processed: 416 average time/residue: 1.5655 time to fit residues: 778.0981 Evaluate side-chains 410 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 367 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 207 optimal weight: 0.0870 chunk 21 optimal weight: 10.0000 chunk 160 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN H 76 GLN K 38 GLN Q 9 GLN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38866 Z= 0.208 Angle : 0.651 16.236 57854 Z= 0.333 Chirality : 0.033 0.277 7310 Planarity : 0.006 0.125 3337 Dihedral : 23.008 179.238 18653 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.66 % Allowed : 37.79 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.21), residues: 1588 helix: 0.91 (0.22), residues: 563 sheet: -0.52 (0.29), residues: 301 loop : -0.27 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.006 0.001 HIS D 198 PHE 0.027 0.002 PHE U 12 TYR 0.026 0.002 TYR D 51 ARG 0.021 0.001 ARG E 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 372 time to evaluate : 2.237 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: D 103 TYR cc_start: 0.9316 (t80) cc_final: 0.8959 (t80) REVERT: D 196 ASN cc_start: 0.8533 (t0) cc_final: 0.8230 (t0) REVERT: E 23 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8113 (mmtt) REVERT: E 33 PHE cc_start: 0.9313 (m-80) cc_final: 0.8928 (m-80) REVERT: E 50 TYR cc_start: 0.9138 (t80) cc_final: 0.8791 (t80) REVERT: F 5 GLU cc_start: 0.8839 (tp30) cc_final: 0.8428 (tp30) REVERT: F 9 MET cc_start: 0.8374 (ptp) cc_final: 0.8034 (mtm) REVERT: F 54 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8719 (tt) REVERT: F 90 MET cc_start: 0.8722 (ttp) cc_final: 0.8387 (mtp) REVERT: H 42 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 118 GLN cc_start: 0.8856 (tt0) cc_final: 0.8539 (tm-30) REVERT: K 14 LYS cc_start: 0.8763 (tmmm) cc_final: 0.7841 (mptt) REVERT: K 15 GLN cc_start: 0.9227 (mm110) cc_final: 0.8934 (mm-40) REVERT: K 64 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8601 (tm-30) REVERT: K 87 LYS cc_start: 0.9355 (ptmm) cc_final: 0.8963 (pttm) REVERT: K 109 ASN cc_start: 0.8389 (t0) cc_final: 0.8061 (p0) REVERT: L 25 GLU cc_start: 0.8316 (mp0) cc_final: 0.8087 (mp0) REVERT: L 47 SER cc_start: 0.8918 (m) cc_final: 0.8588 (p) REVERT: P 76 LYS cc_start: 0.8933 (tttt) cc_final: 0.8621 (tttt) REVERT: R 33 ILE cc_start: 0.9488 (pt) cc_final: 0.9169 (pp) REVERT: R 47 THR cc_start: 0.9552 (m) cc_final: 0.9144 (t) REVERT: R 51 TYR cc_start: 0.9022 (m-80) cc_final: 0.8644 (m-10) REVERT: U 4 ILE cc_start: 0.8378 (pp) cc_final: 0.7071 (pt) REVERT: U 20 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8796 (tmmm) REVERT: U 24 GLU cc_start: 0.8947 (pm20) cc_final: 0.8590 (pm20) REVERT: U 25 LYS cc_start: 0.9459 (mmtt) cc_final: 0.9170 (tmmt) REVERT: U 56 HIS cc_start: 0.9280 (t70) cc_final: 0.9074 (t70) REVERT: W 152 GLN cc_start: 0.9322 (mm110) cc_final: 0.9019 (mp10) REVERT: W 167 ASP cc_start: 0.8315 (p0) cc_final: 0.7943 (m-30) REVERT: W 282 GLN cc_start: 0.9223 (mt0) cc_final: 0.8937 (mt0) outliers start: 49 outliers final: 47 residues processed: 399 average time/residue: 1.5180 time to fit residues: 724.1314 Evaluate side-chains 409 residues out of total 1339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 361 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 211 ILE Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN T 52 ASN T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.035457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.028097 restraints weight = 212356.447| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 1.83 r_work: 0.2396 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 38866 Z= 0.381 Angle : 0.712 16.447 57854 Z= 0.366 Chirality : 0.037 0.289 7310 Planarity : 0.006 0.129 3337 Dihedral : 23.043 176.778 18653 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.63 % Allowed : 36.89 % Favored : 58.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.21), residues: 1588 helix: 0.73 (0.22), residues: 570 sheet: -0.77 (0.29), residues: 310 loop : -0.29 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 60 HIS 0.005 0.001 HIS D 198 PHE 0.028 0.002 PHE U 12 TYR 0.030 0.002 TYR D 51 ARG 0.012 0.001 ARG F 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12530.97 seconds wall clock time: 223 minutes 5.69 seconds (13385.69 seconds total)