Starting phenix.real_space_refine on Fri Feb 23 21:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r90_4764/02_2024/6r90_4764_trim_updated.pdb" } resolution = 4.5 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= -0.003 sd= 0.767 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: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 66 5.16 5 C 12543 2.51 5 N 3818 2.21 5 O 4553 1.98 5 H 18802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ASP 125": "OD1" <-> "OD2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "K PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 166": "OD1" <-> "OD2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K GLU 288": "OE1" <-> "OE2" Residue "K ASP 299": "OD1" <-> "OD2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K GLU 307": "OE1" <-> "OE2" Residue "K ASP 330": "OD1" <-> "OD2" Residue "K ASP 339": "OD1" <-> "OD2" Residue "K ASP 366": "OD1" <-> "OD2" Residue "K GLU 368": "OE1" <-> "OE2" Residue "K GLU 719": "OE1" <-> "OE2" Residue "K PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 744": "OD1" <-> "OD2" Residue "K GLU 785": "OE1" <-> "OE2" Residue "K GLU 787": "OE1" <-> "OE2" Residue "K GLU 839": "OE1" <-> "OE2" Residue "K GLU 840": "OE1" <-> "OE2" Residue "K GLU 875": "OE1" <-> "OE2" Residue "K GLU 898": "OE1" <-> "OE2" Residue "K GLU 944": "OE1" <-> "OE2" Residue "K PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 969": "OE1" <-> "OE2" Residue "K ASP 986": "OD1" <-> "OD2" Residue "K GLU 987": "OE1" <-> "OE2" Residue "K GLU 988": "OE1" <-> "OE2" Residue "K GLU 994": "OE1" <-> "OE2" Residue "K ASP 1053": "OD1" <-> "OD2" Residue "K GLU 1079": "OE1" <-> "OE2" Residue "K GLU 1095": "OE1" <-> "OE2" Residue "K GLU 1123": "OE1" <-> "OE2" Residue "K ASP 1127": "OD1" <-> "OD2" Residue "K GLU 1134": "OE1" <-> "OE2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 135": "OD1" <-> "OD2" Residue "L ASP 145": "OD1" <-> "OD2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 198": "OD1" <-> "OD2" Residue "L PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 373": "OD1" <-> "OD2" Residue "L ASP 376": "OD1" <-> "OD2" Residue "L TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1614 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1269 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1730 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1457 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1681 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1456 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1663 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1446 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4565 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "K" Number of atoms: 12898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12898 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5680 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 22, 'TRANS': 342} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 18.94, per 1000 atoms: 0.47 Number of scatterers: 40070 At special positions: 0 Unit cell: (152.22, 173.72, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 288 15.00 O 4553 8.00 N 3818 7.00 C 12543 6.00 H 18802 1.00 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: 33.67 Conformation dependent library (CDL) restraints added in 3.2 seconds 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 23 sheets defined 30.2% alpha, 21.6% beta 143 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 25.57 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.757A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.677A pdb=" N TYR B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 71 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 Processing helix chain 'E' and resid 87 through 115 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 26 through 29 Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 51 through 76 removed outlier: 3.520A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 251 through 255 removed outlier: 3.993A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 756 through 758 No H-bonds generated for 'chain 'K' and resid 756 through 758' Processing helix chain 'K' and resid 769 through 771 No H-bonds generated for 'chain 'K' and resid 769 through 771' Processing helix chain 'K' and resid 986 through 989 No H-bonds generated for 'chain 'K' and resid 986 through 989' Processing helix chain 'K' and resid 1045 through 1059 Processing helix chain 'K' and resid 1070 through 1074 Processing helix chain 'K' and resid 1091 through 1099 removed outlier: 3.756A pdb=" N PHE K1097 " --> pdb=" O LEU K1093 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU K1098 " --> pdb=" O ILE K1094 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP K1099 " --> pdb=" O GLU K1095 " (cutoff:3.500A) Processing helix chain 'K' and resid 1102 through 1108 Processing helix chain 'K' and resid 1126 through 1139 removed outlier: 3.586A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE K1139 " --> pdb=" O GLU K1135 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 78 Processing helix chain 'L' and resid 83 through 100 removed outlier: 4.000A pdb=" N SER L 100 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 1088 through 1090 removed outlier: 7.217A pdb=" N ASN K 4 " --> pdb=" O ILE K1089 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR K 3 " --> pdb=" O LEU K1043 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 17 through 21 removed outlier: 6.150A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 61 through 67 removed outlier: 6.558A pdb=" N LEU K 80 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET K 64 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE K 78 " --> pdb=" O MET K 64 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU K 66 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU K 76 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 121 through 124 Processing sheet with id= E, first strand: chain 'K' and resid 201 through 204 removed outlier: 6.198A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 218 through 221 Processing sheet with id= G, first strand: chain 'K' and resid 258 through 263 removed outlier: 6.924A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N MET K 282 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU K 304 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU K 284 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL K 302 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU K 286 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU K 300 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 287 through 289 Processing sheet with id= I, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.770A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS K 335 " --> pdb=" O ALA K 349 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA K 349 " --> pdb=" O LYS K 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 711 through 716 removed outlier: 3.998A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 724 through 727 removed outlier: 3.525A pdb=" N CYS K 732 " --> pdb=" O GLN K 727 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 741 through 743 Processing sheet with id= M, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.736A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 872 through 876 removed outlier: 3.778A pdb=" N SER K 872 " --> pdb=" O SER K 883 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS K 903 " --> pdb=" O LEU K 890 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU K 892 " --> pdb=" O THR K 901 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR K 901 " --> pdb=" O GLU K 892 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 911 through 917 removed outlier: 6.494A pdb=" N GLY K 924 " --> pdb=" O LEU K 912 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU K 914 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU K 922 " --> pdb=" O LEU K 914 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR K 916 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE K 920 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS K 936 " --> pdb=" O PHE K 942 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE K 942 " --> pdb=" O LYS K 936 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 954 through 959 removed outlier: 6.844A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= R, first strand: chain 'L' and resid 148 through 150 Processing sheet with id= S, first strand: chain 'L' and resid 171 through 174 removed outlier: 6.569A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 225 through 228 Processing sheet with id= U, first strand: chain 'L' and resid 283 through 286 removed outlier: 4.802A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 325 through 327 removed outlier: 3.626A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA L 293 " --> pdb=" O THR L 306 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 350 through 354 removed outlier: 3.742A pdb=" N CYS L 384 " --> pdb=" O VAL L 374 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 688 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 19.21 Time building geometry restraints manager: 34.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18776 1.03 - 1.22: 136 1.22 - 1.42: 9568 1.42 - 1.62: 12481 1.62 - 1.82: 107 Bond restraints: 41068 Sorted by residual: bond pdb=" C4' 3DR J 94 " pdb=" O4' 3DR J 94 " ideal model delta sigma weight residual 1.664 1.437 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4' 3DR J 93 " pdb=" O4' 3DR J 93 " ideal model delta sigma weight residual 1.664 1.441 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4' 3DR J 93 " pdb=" C3' 3DR J 93 " ideal model delta sigma weight residual 1.336 1.533 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C4' 3DR J 94 " pdb=" C3' 3DR J 94 " ideal model delta sigma weight residual 1.336 1.524 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" O4' 3DR J 94 " pdb=" C1' 3DR J 94 " ideal model delta sigma weight residual 1.309 1.427 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 41063 not shown) Histogram of bond angle deviations from ideal: 73.33 - 85.47: 6 85.47 - 97.61: 0 97.61 - 109.75: 31210 109.75 - 121.89: 35573 121.89 - 134.03: 7571 Bond angle restraints: 74360 Sorted by residual: angle pdb=" CB CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 109.00 74.85 34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N CYS L 66 " pdb=" CA CYS L 66 " pdb=" HA CYS L 66 " ideal model delta sigma weight residual 110.00 76.13 33.87 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CD2 LEU L 63 " pdb=" CG LEU L 63 " pdb=" HG LEU L 63 " ideal model delta sigma weight residual 108.00 83.69 24.31 3.00e+00 1.11e-01 6.57e+01 angle pdb=" CB LEU L 63 " pdb=" CG LEU L 63 " pdb=" HG LEU L 63 " ideal model delta sigma weight residual 109.00 85.37 23.63 3.00e+00 1.11e-01 6.20e+01 ... (remaining 74355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 16273 34.73 - 69.46: 1855 69.46 - 104.19: 44 104.19 - 138.92: 0 138.92 - 173.66: 4 Dihedral angle restraints: 18176 sinusoidal: 11759 harmonic: 6417 Sorted by residual: dihedral pdb=" CA ILE K 884 " pdb=" C ILE K 884 " pdb=" N ASN K 885 " pdb=" CA ASN K 885 " ideal model delta harmonic sigma weight residual -180.00 -148.14 -31.86 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ARG K 847 " pdb=" C ARG K 847 " pdb=" N ILE K 848 " pdb=" CA ILE K 848 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 18173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 3541 0.340 - 0.680: 1 0.680 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.699: 1 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" CA CYS L 66 " pdb=" N CYS L 66 " pdb=" C CYS L 66 " pdb=" CB CYS L 66 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' 3DR J 94 " pdb=" C4' 3DR J 94 " pdb=" O3' 3DR J 94 " pdb=" C2' 3DR J 94 " both_signs ideal model delta sigma weight residual False -2.43 -2.66 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3540 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 382 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C PHE K 382 " 0.090 2.00e-02 2.50e+03 pdb=" O PHE K 382 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS K 383 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 381 " 0.025 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C ALA K 381 " -0.089 2.00e-02 2.50e+03 pdb=" O ALA K 381 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE K 382 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS L 146 " 0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO L 147 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " 0.044 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 4161 2.24 - 2.83: 83250 2.83 - 3.42: 101247 3.42 - 4.01: 146417 4.01 - 4.60: 214589 Nonbonded interactions: 549664 Sorted by model distance: nonbonded pdb=" OD1 ASN K 36 " pdb=" HZ2 LYS K 60 " model vdw 1.652 1.850 nonbonded pdb=" O ARG L 113 " pdb=" H LYS L 132 " model vdw 1.653 1.850 nonbonded pdb=" HE ARG E 70 " pdb=" OD1 ASN F 26 " model vdw 1.657 1.850 nonbonded pdb=" O LEU E 104 " pdb=" HG1 THR E 108 " model vdw 1.657 1.850 nonbonded pdb=" O HIS F 76 " pdb="HH12 ARG H 93 " model vdw 1.660 1.850 ... (remaining 549659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name HD \ 21 or name HD22)) or resid 27 through 102)) } ncs_group { reference = (chain 'C' and ((resid 16 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 17 through 76 or (resid 77 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA or nam \ e HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid 78 through 11 \ 9)) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 34 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 35 through 124) \ ) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.580 Extract box with map and model: 8.110 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 148.100 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 0.227 22266 Z= 0.431 Angle : 0.880 12.058 31343 Z= 0.516 Chirality : 0.055 1.699 3543 Planarity : 0.006 0.081 2998 Dihedral : 22.921 173.656 9112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.07 % Favored : 96.62 % Rotamer: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.17), residues: 1922 helix: 0.56 (0.18), residues: 638 sheet: -0.72 (0.23), residues: 465 loop : -1.77 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 207 HIS 0.006 0.001 HIS L 345 PHE 0.033 0.003 PHE K 382 TYR 0.024 0.002 TYR K 245 ARG 0.008 0.001 ARG L 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 585 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8148 (mm-30) REVERT: A 53 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8372 (mtt90) REVERT: A 57 LYS cc_start: 0.9420 (tttt) cc_final: 0.9022 (tppt) REVERT: A 70 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7928 (mtm110) REVERT: A 74 GLU cc_start: 0.8425 (tt0) cc_final: 0.8162 (tt0) REVERT: A 106 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7797 (tp30) REVERT: B 38 LEU cc_start: 0.9385 (mt) cc_final: 0.9038 (mt) REVERT: B 99 TYR cc_start: 0.8632 (m-10) cc_final: 0.8397 (m-10) REVERT: C 40 TYR cc_start: 0.8573 (m-80) cc_final: 0.8038 (m-10) REVERT: C 96 LYS cc_start: 0.8832 (tptt) cc_final: 0.8241 (ttmm) REVERT: C 111 ASN cc_start: 0.8947 (t0) cc_final: 0.8728 (t0) REVERT: D 44 LYS cc_start: 0.8882 (mttt) cc_final: 0.8499 (mtmt) REVERT: D 96 GLN cc_start: 0.9053 (tt0) cc_final: 0.8810 (tt0) REVERT: D 100 ARG cc_start: 0.8660 (mtt90) cc_final: 0.8229 (tpp80) REVERT: D 109 LYS cc_start: 0.9181 (mttt) cc_final: 0.8610 (mmmt) REVERT: D 116 THR cc_start: 0.9143 (m) cc_final: 0.8929 (p) REVERT: E 61 LEU cc_start: 0.9179 (mt) cc_final: 0.8898 (mt) REVERT: E 98 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7879 (pp20) REVERT: E 110 LEU cc_start: 0.9485 (mt) cc_final: 0.9250 (tp) REVERT: F 60 LYS cc_start: 0.7780 (tttt) cc_final: 0.7552 (ttmm) REVERT: F 89 TYR cc_start: 0.8681 (m-10) cc_final: 0.8474 (m-80) REVERT: G 39 ASN cc_start: 0.8811 (m110) cc_final: 0.8565 (p0) REVERT: G 63 ILE cc_start: 0.9127 (mt) cc_final: 0.8914 (tp) REVERT: H 94 GLU cc_start: 0.8990 (mp0) cc_final: 0.8486 (mp0) REVERT: H 97 THR cc_start: 0.9456 (m) cc_final: 0.9236 (p) REVERT: H 101 LEU cc_start: 0.9164 (mt) cc_final: 0.8533 (mt) REVERT: H 117 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8423 (ttpt) REVERT: K 87 CYS cc_start: 0.6383 (p) cc_final: 0.6122 (m) REVERT: K 152 LEU cc_start: 0.8616 (mt) cc_final: 0.8227 (mt) REVERT: K 166 ASP cc_start: 0.7317 (m-30) cc_final: 0.6782 (m-30) REVERT: K 194 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7866 (tm-30) REVERT: K 203 ASN cc_start: 0.7238 (m110) cc_final: 0.6389 (m110) REVERT: K 217 SER cc_start: 0.7990 (p) cc_final: 0.7715 (t) REVERT: K 234 GLN cc_start: 0.8645 (tp40) cc_final: 0.8074 (tt0) REVERT: K 235 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8184 (tm-30) REVERT: K 330 ASP cc_start: 0.3659 (m-30) cc_final: 0.3203 (m-30) REVERT: K 378 CYS cc_start: 0.7740 (m) cc_final: 0.7409 (m) REVERT: K 379 SER cc_start: 0.7821 (t) cc_final: 0.7015 (p) REVERT: K 755 SER cc_start: 0.7966 (p) cc_final: 0.7668 (m) REVERT: K 787 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6559 (mt-10) REVERT: K 969 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8307 (tm-30) REVERT: K 1014 MET cc_start: 0.2502 (tpp) cc_final: 0.1535 (pmm) REVERT: K 1030 PHE cc_start: 0.7556 (p90) cc_final: 0.7355 (p90) REVERT: K 1102 ARG cc_start: 0.9049 (ttt90) cc_final: 0.8391 (mpt180) REVERT: L 88 GLN cc_start: 0.8506 (mt0) cc_final: 0.8072 (tt0) REVERT: L 123 HIS cc_start: 0.8188 (t-90) cc_final: 0.6936 (t-90) REVERT: L 240 MET cc_start: 0.7829 (mtt) cc_final: 0.7615 (mtt) REVERT: L 356 TYR cc_start: 0.8083 (t80) cc_final: 0.7725 (t80) REVERT: L 357 PRO cc_start: 0.8823 (Cg_exo) cc_final: 0.8478 (Cg_endo) REVERT: L 360 ASN cc_start: 0.9474 (m-40) cc_final: 0.9130 (p0) REVERT: L 373 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5693 (t70) REVERT: L 388 ASP cc_start: 0.7156 (t70) cc_final: 0.6946 (t0) REVERT: L 398 ASN cc_start: 0.7137 (t0) cc_final: 0.6644 (t0) outliers start: 4 outliers final: 2 residues processed: 587 average time/residue: 0.8781 time to fit residues: 741.2543 Evaluate side-chains 451 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 448 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 859 GLN K 904 ASN K1016 ASN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1055 GLN K1111 ASN L 91 GLN L 92 GLN L 170 ASN L 319 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 22266 Z= 0.343 Angle : 0.729 11.424 31343 Z= 0.430 Chirality : 0.054 1.667 3543 Planarity : 0.005 0.054 2998 Dihedral : 26.253 171.914 5366 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.84 (0.18), residues: 1922 helix: 0.70 (0.20), residues: 634 sheet: -0.63 (0.23), residues: 459 loop : -1.46 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 203 HIS 0.006 0.001 HIS E 114 PHE 0.029 0.002 PHE L 257 TYR 0.018 0.002 TYR K 245 ARG 0.007 0.001 ARG L 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8509 (mm-30) REVERT: A 55 TYR cc_start: 0.8962 (m-80) cc_final: 0.8751 (m-10) REVERT: A 57 LYS cc_start: 0.9536 (tttt) cc_final: 0.9258 (tppt) REVERT: A 61 LEU cc_start: 0.9233 (mt) cc_final: 0.9030 (mt) REVERT: A 70 ARG cc_start: 0.8349 (mtm110) cc_final: 0.7861 (mtm110) REVERT: A 98 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7524 (mm-30) REVERT: A 106 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8225 (tp30) REVERT: C 40 TYR cc_start: 0.8852 (m-80) cc_final: 0.8261 (m-10) REVERT: C 96 LYS cc_start: 0.8982 (tptt) cc_final: 0.8388 (ttmm) REVERT: D 100 ARG cc_start: 0.8738 (mtt90) cc_final: 0.8405 (tpp80) REVERT: D 109 LYS cc_start: 0.9254 (mttt) cc_final: 0.8618 (tppt) REVERT: E 61 LEU cc_start: 0.9417 (mt) cc_final: 0.9116 (mt) REVERT: E 94 GLN cc_start: 0.9137 (tt0) cc_final: 0.8734 (tt0) REVERT: E 98 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7684 (pp20) REVERT: E 100 TYR cc_start: 0.9173 (t80) cc_final: 0.8783 (t80) REVERT: F 75 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8642 (tt0) REVERT: H 63 MET cc_start: 0.8940 (mmm) cc_final: 0.8373 (mmm) REVERT: H 94 GLU cc_start: 0.9127 (mp0) cc_final: 0.8736 (mp0) REVERT: H 106 GLU cc_start: 0.9031 (mp0) cc_final: 0.8703 (mp0) REVERT: H 117 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8500 (ttpt) REVERT: K 4 ASN cc_start: 0.8339 (m-40) cc_final: 0.7851 (m-40) REVERT: K 124 ILE cc_start: 0.8444 (mt) cc_final: 0.8169 (tt) REVERT: K 152 LEU cc_start: 0.8639 (mt) cc_final: 0.8317 (mt) REVERT: K 235 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8024 (tm-30) REVERT: K 366 ASP cc_start: 0.7370 (p0) cc_final: 0.7140 (p0) REVERT: K 842 GLU cc_start: 0.5957 (mm-30) cc_final: 0.5215 (mm-30) REVERT: K 879 LYS cc_start: 0.7879 (mttt) cc_final: 0.7601 (mmtt) REVERT: K 1030 PHE cc_start: 0.7761 (p90) cc_final: 0.7392 (p90) REVERT: K 1102 ARG cc_start: 0.9180 (ttt90) cc_final: 0.8366 (mpt180) REVERT: K 1105 MET cc_start: 0.7106 (mtt) cc_final: 0.6548 (mtt) REVERT: L 88 GLN cc_start: 0.8544 (mt0) cc_final: 0.8171 (tt0) REVERT: L 123 HIS cc_start: 0.8300 (t-90) cc_final: 0.6922 (t-90) REVERT: L 215 MET cc_start: 0.7536 (mtp) cc_final: 0.7292 (mmt) REVERT: L 332 ARG cc_start: 0.8737 (tpt-90) cc_final: 0.8454 (tpt-90) REVERT: L 340 ILE cc_start: 0.8905 (mt) cc_final: 0.8700 (mm) REVERT: L 388 ASP cc_start: 0.7753 (t70) cc_final: 0.7519 (t0) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.8360 time to fit residues: 626.2925 Evaluate side-chains 430 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 158 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN C 90 ASN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22266 Z= 0.223 Angle : 0.640 10.877 31343 Z= 0.379 Chirality : 0.051 1.652 3543 Planarity : 0.004 0.058 2998 Dihedral : 26.121 172.350 5366 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.49 (0.19), residues: 1922 helix: 1.00 (0.20), residues: 637 sheet: -0.37 (0.24), residues: 469 loop : -1.33 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 203 HIS 0.011 0.001 HIS L 74 PHE 0.022 0.001 PHE L 257 TYR 0.016 0.001 TYR H 41 ARG 0.007 0.000 ARG K 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9514 (tttt) cc_final: 0.9225 (tppt) REVERT: A 62 LEU cc_start: 0.9620 (mt) cc_final: 0.9316 (mt) REVERT: A 70 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7774 (mtm110) REVERT: A 80 LYS cc_start: 0.7668 (tttp) cc_final: 0.7336 (mptt) REVERT: A 98 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7834 (mm-30) REVERT: A 106 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8145 (tp30) REVERT: B 99 TYR cc_start: 0.8776 (m-10) cc_final: 0.8499 (m-10) REVERT: C 39 ASN cc_start: 0.8506 (m-40) cc_final: 0.8091 (m-40) REVERT: C 42 GLU cc_start: 0.8102 (mp0) cc_final: 0.7478 (mp0) REVERT: C 43 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8424 (mtt180) REVERT: C 69 ASN cc_start: 0.9199 (m110) cc_final: 0.8916 (m-40) REVERT: C 96 LYS cc_start: 0.8932 (tptt) cc_final: 0.8372 (ttmm) REVERT: D 52 ASP cc_start: 0.9076 (p0) cc_final: 0.8860 (p0) REVERT: D 100 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8337 (tpp80) REVERT: D 109 LYS cc_start: 0.9082 (mttt) cc_final: 0.8525 (tppp) REVERT: E 61 LEU cc_start: 0.9409 (mt) cc_final: 0.9030 (mt) REVERT: E 97 CYS cc_start: 0.8875 (m) cc_final: 0.8534 (t) REVERT: E 98 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7872 (pp20) REVERT: E 100 TYR cc_start: 0.9134 (t80) cc_final: 0.8757 (t80) REVERT: F 75 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8640 (tt0) REVERT: F 85 MET cc_start: 0.8387 (mmt) cc_final: 0.8163 (mmp) REVERT: H 63 MET cc_start: 0.8922 (mmm) cc_final: 0.8269 (mmm) REVERT: H 90 ILE cc_start: 0.7234 (mt) cc_final: 0.7029 (tp) REVERT: H 94 GLU cc_start: 0.9065 (mp0) cc_final: 0.8672 (mp0) REVERT: H 106 GLU cc_start: 0.9012 (mp0) cc_final: 0.8642 (mp0) REVERT: H 107 LEU cc_start: 0.8999 (mt) cc_final: 0.8707 (mt) REVERT: H 117 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8386 (ttpt) REVERT: K 4 ASN cc_start: 0.8366 (m-40) cc_final: 0.7746 (m-40) REVERT: K 124 ILE cc_start: 0.8415 (mt) cc_final: 0.8169 (tt) REVERT: K 152 LEU cc_start: 0.8556 (mt) cc_final: 0.8310 (mp) REVERT: K 166 ASP cc_start: 0.7278 (m-30) cc_final: 0.7066 (m-30) REVERT: K 235 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8234 (tm-30) REVERT: K 343 GLN cc_start: 0.8950 (tp40) cc_final: 0.8336 (tm-30) REVERT: K 366 ASP cc_start: 0.7368 (p0) cc_final: 0.7128 (p0) REVERT: K 986 ASP cc_start: 0.9148 (t70) cc_final: 0.8931 (t70) REVERT: K 1007 PHE cc_start: 0.7432 (m-80) cc_final: 0.6979 (m-80) REVERT: K 1102 ARG cc_start: 0.9169 (ttt90) cc_final: 0.8465 (mpt180) REVERT: L 88 GLN cc_start: 0.8531 (mt0) cc_final: 0.8170 (tt0) REVERT: L 123 HIS cc_start: 0.8676 (t-90) cc_final: 0.7212 (t-90) REVERT: L 340 ILE cc_start: 0.8942 (mt) cc_final: 0.8693 (mm) REVERT: L 388 ASP cc_start: 0.7717 (t70) cc_final: 0.7348 (t0) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.8254 time to fit residues: 608.7102 Evaluate side-chains 443 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 0.0270 chunk 209 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 109 ASN D 48 GLN ** K 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 993 GLN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22266 Z= 0.216 Angle : 0.624 10.762 31343 Z= 0.370 Chirality : 0.051 1.641 3543 Planarity : 0.004 0.063 2998 Dihedral : 26.104 172.455 5366 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 1.56 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.52 (0.19), residues: 1922 helix: 0.92 (0.20), residues: 643 sheet: -0.43 (0.24), residues: 459 loop : -1.26 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 203 HIS 0.010 0.001 HIS L 74 PHE 0.021 0.001 PHE L 141 TYR 0.016 0.001 TYR H 41 ARG 0.011 0.001 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9520 (tttt) cc_final: 0.9226 (tppt) REVERT: A 62 LEU cc_start: 0.9605 (mt) cc_final: 0.9313 (mt) REVERT: A 70 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7842 (mtm110) REVERT: A 98 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7809 (mm-30) REVERT: A 106 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8147 (tp30) REVERT: B 53 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7989 (tm-30) REVERT: B 85 MET cc_start: 0.7328 (mmm) cc_final: 0.7110 (mmm) REVERT: B 99 TYR cc_start: 0.8759 (m-10) cc_final: 0.8515 (m-10) REVERT: C 34 LEU cc_start: 0.8569 (tp) cc_final: 0.8283 (tp) REVERT: C 37 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8879 (ttmm) REVERT: C 39 ASN cc_start: 0.8520 (m-40) cc_final: 0.8210 (m-40) REVERT: C 42 GLU cc_start: 0.8161 (mp0) cc_final: 0.7573 (mp0) REVERT: C 69 ASN cc_start: 0.9201 (m110) cc_final: 0.8911 (m-40) REVERT: C 96 LYS cc_start: 0.8941 (tptt) cc_final: 0.8543 (tppt) REVERT: D 100 ARG cc_start: 0.8712 (mtt90) cc_final: 0.8419 (tpp80) REVERT: D 109 LYS cc_start: 0.9055 (mttt) cc_final: 0.8539 (tppp) REVERT: E 61 LEU cc_start: 0.9450 (mt) cc_final: 0.9022 (mt) REVERT: E 97 CYS cc_start: 0.8915 (m) cc_final: 0.8478 (t) REVERT: E 98 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7906 (pp20) REVERT: F 75 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8824 (tt0) REVERT: F 85 MET cc_start: 0.8431 (mmt) cc_final: 0.8164 (mmp) REVERT: H 106 GLU cc_start: 0.8998 (mp0) cc_final: 0.8604 (mp0) REVERT: H 107 LEU cc_start: 0.8935 (mt) cc_final: 0.8638 (mt) REVERT: H 117 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8361 (ttpt) REVERT: K 124 ILE cc_start: 0.8434 (mt) cc_final: 0.8171 (tt) REVERT: K 152 LEU cc_start: 0.8517 (mt) cc_final: 0.8282 (mp) REVERT: K 215 GLU cc_start: 0.9154 (tp30) cc_final: 0.8545 (tp30) REVERT: K 235 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8299 (tm-30) REVERT: K 327 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8513 (ttm110) REVERT: K 343 GLN cc_start: 0.8963 (tp40) cc_final: 0.8329 (tm-30) REVERT: K 366 ASP cc_start: 0.7379 (p0) cc_final: 0.7098 (p0) REVERT: K 787 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6381 (mt-10) REVERT: K 842 GLU cc_start: 0.6234 (mm-30) cc_final: 0.5103 (mp0) REVERT: K 986 ASP cc_start: 0.9141 (t70) cc_final: 0.8929 (t70) REVERT: K 1041 THR cc_start: 0.7510 (p) cc_final: 0.7260 (t) REVERT: K 1102 ARG cc_start: 0.9176 (ttt90) cc_final: 0.8447 (mpt180) REVERT: L 88 GLN cc_start: 0.8542 (mt0) cc_final: 0.8195 (tt0) REVERT: L 123 HIS cc_start: 0.8781 (t-90) cc_final: 0.7292 (t-90) REVERT: L 177 MET cc_start: 0.8085 (ttm) cc_final: 0.7722 (tpp) REVERT: L 270 TRP cc_start: 0.6032 (m100) cc_final: 0.5763 (m100) REVERT: L 340 ILE cc_start: 0.8963 (mt) cc_final: 0.8723 (mm) REVERT: L 382 MET cc_start: 0.6967 (mtm) cc_final: 0.6715 (mtt) REVERT: L 388 ASP cc_start: 0.7846 (t70) cc_final: 0.7512 (t0) REVERT: L 409 SER cc_start: 0.7722 (m) cc_final: 0.7519 (m) outliers start: 2 outliers final: 0 residues processed: 498 average time/residue: 0.7827 time to fit residues: 577.0239 Evaluate side-chains 435 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 885 ASN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 22266 Z= 0.384 Angle : 0.738 10.877 31343 Z= 0.439 Chirality : 0.055 1.639 3543 Planarity : 0.005 0.053 2998 Dihedral : 26.284 173.707 5366 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.38 (0.18), residues: 1922 helix: -0.29 (0.19), residues: 636 sheet: -0.53 (0.24), residues: 468 loop : -1.57 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 203 HIS 0.007 0.002 HIS L 74 PHE 0.021 0.002 PHE L 296 TYR 0.025 0.002 TYR G 40 ARG 0.007 0.001 ARG K 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 490 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9557 (tttt) cc_final: 0.9274 (tppt) REVERT: A 70 ARG cc_start: 0.8416 (mtm110) cc_final: 0.8107 (mtm110) REVERT: A 97 CYS cc_start: 0.9225 (m) cc_final: 0.8045 (t) REVERT: A 98 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7859 (mm-30) REVERT: A 106 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8235 (tp30) REVERT: B 37 ARG cc_start: 0.9090 (mtm-85) cc_final: 0.8718 (mtm180) REVERT: B 53 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8129 (tm-30) REVERT: C 37 LYS cc_start: 0.9403 (ttmm) cc_final: 0.9069 (ttmm) REVERT: C 42 GLU cc_start: 0.8448 (mp0) cc_final: 0.7909 (mp0) REVERT: C 43 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8297 (mtt180) REVERT: C 69 ASN cc_start: 0.9142 (m110) cc_final: 0.8913 (m-40) REVERT: C 96 LYS cc_start: 0.9022 (tptt) cc_final: 0.8678 (tppt) REVERT: D 100 ARG cc_start: 0.8887 (mtt90) cc_final: 0.8505 (tpp80) REVERT: D 109 LYS cc_start: 0.9178 (mttt) cc_final: 0.8693 (tppp) REVERT: E 61 LEU cc_start: 0.9504 (mt) cc_final: 0.9207 (mt) REVERT: E 94 GLN cc_start: 0.9112 (tt0) cc_final: 0.8844 (tt0) REVERT: E 97 CYS cc_start: 0.8944 (m) cc_final: 0.8588 (t) REVERT: E 98 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7932 (pp20) REVERT: E 117 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7703 (ttp-170) REVERT: F 75 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8968 (tt0) REVERT: H 63 MET cc_start: 0.8772 (mmm) cc_final: 0.8397 (mmm) REVERT: H 106 GLU cc_start: 0.9129 (mp0) cc_final: 0.8889 (mp0) REVERT: H 107 LEU cc_start: 0.9041 (mt) cc_final: 0.8774 (mt) REVERT: H 117 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8491 (ttpt) REVERT: K 47 GLU cc_start: 0.8118 (tp30) cc_final: 0.7694 (pm20) REVERT: K 152 LEU cc_start: 0.8526 (mt) cc_final: 0.8219 (mt) REVERT: K 215 GLU cc_start: 0.9227 (tp30) cc_final: 0.8732 (tp30) REVERT: K 235 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8354 (tm-30) REVERT: K 366 ASP cc_start: 0.7352 (p0) cc_final: 0.7063 (p0) REVERT: K 879 LYS cc_start: 0.8240 (mttt) cc_final: 0.7972 (mttm) REVERT: K 1014 MET cc_start: 0.2620 (tpp) cc_final: 0.0738 (pmm) REVERT: K 1102 ARG cc_start: 0.9229 (ttt90) cc_final: 0.8528 (mpt180) REVERT: L 88 GLN cc_start: 0.8622 (mt0) cc_final: 0.8290 (tt0) REVERT: L 101 TYR cc_start: 0.8337 (m-10) cc_final: 0.7813 (m-10) REVERT: L 120 HIS cc_start: 0.8314 (t-170) cc_final: 0.8038 (t-170) REVERT: L 270 TRP cc_start: 0.6284 (m100) cc_final: 0.5810 (m100) REVERT: L 382 MET cc_start: 0.7354 (mtm) cc_final: 0.6975 (mtt) REVERT: L 388 ASP cc_start: 0.8033 (t70) cc_final: 0.7799 (t0) REVERT: L 409 SER cc_start: 0.7672 (m) cc_final: 0.7372 (m) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.8182 time to fit residues: 591.1132 Evaluate side-chains 433 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 255 GLN ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22266 Z= 0.239 Angle : 0.648 10.771 31343 Z= 0.384 Chirality : 0.051 1.634 3543 Planarity : 0.004 0.068 2998 Dihedral : 26.284 173.123 5366 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.99 (0.19), residues: 1922 helix: 0.31 (0.20), residues: 630 sheet: -0.44 (0.25), residues: 453 loop : -1.49 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 203 HIS 0.007 0.001 HIS L 74 PHE 0.034 0.002 PHE K1007 TYR 0.017 0.001 TYR H 41 ARG 0.020 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7217 (mmm160) REVERT: A 57 LYS cc_start: 0.9519 (tttt) cc_final: 0.9232 (tppt) REVERT: A 70 ARG cc_start: 0.8290 (mtm110) cc_final: 0.7959 (mtm110) REVERT: A 98 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7775 (mm-30) REVERT: A 106 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8174 (tp30) REVERT: B 53 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8035 (tm-30) REVERT: C 37 LYS cc_start: 0.9521 (ttmm) cc_final: 0.9059 (ttmm) REVERT: C 42 GLU cc_start: 0.8436 (mp0) cc_final: 0.7977 (mp0) REVERT: C 69 ASN cc_start: 0.9081 (m110) cc_final: 0.8820 (m-40) REVERT: C 96 LYS cc_start: 0.8938 (tptt) cc_final: 0.8563 (tppt) REVERT: C 111 ASN cc_start: 0.9095 (t0) cc_final: 0.8892 (t0) REVERT: D 100 ARG cc_start: 0.8863 (mtt90) cc_final: 0.8610 (tpp80) REVERT: D 109 LYS cc_start: 0.9113 (mttt) cc_final: 0.8589 (tppp) REVERT: E 61 LEU cc_start: 0.9532 (mt) cc_final: 0.9178 (mt) REVERT: E 97 CYS cc_start: 0.8944 (m) cc_final: 0.8452 (t) REVERT: E 98 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7873 (pp20) REVERT: E 121 MET cc_start: 0.8139 (mtt) cc_final: 0.7880 (mtm) REVERT: F 75 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8899 (tt0) REVERT: G 51 TYR cc_start: 0.9176 (t80) cc_final: 0.8762 (t80) REVERT: H 48 GLN cc_start: 0.7971 (tt0) cc_final: 0.7600 (tm-30) REVERT: H 96 GLN cc_start: 0.9345 (tt0) cc_final: 0.8626 (tp40) REVERT: H 101 LEU cc_start: 0.8703 (mt) cc_final: 0.8424 (mt) REVERT: H 117 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8418 (ttpt) REVERT: K 47 GLU cc_start: 0.8104 (tp30) cc_final: 0.7878 (pm20) REVERT: K 152 LEU cc_start: 0.8495 (mt) cc_final: 0.8171 (mt) REVERT: K 215 GLU cc_start: 0.9222 (tp30) cc_final: 0.8699 (tp30) REVERT: K 235 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8488 (tm-30) REVERT: K 312 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6872 (tm-30) REVERT: K 327 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8678 (ttp80) REVERT: K 343 GLN cc_start: 0.8966 (tp40) cc_final: 0.8242 (tm-30) REVERT: K 366 ASP cc_start: 0.7390 (p0) cc_final: 0.7136 (p0) REVERT: K 736 LEU cc_start: 0.8546 (mt) cc_final: 0.8293 (mt) REVERT: K 908 ASN cc_start: 0.9269 (m-40) cc_final: 0.9067 (m-40) REVERT: K 914 LEU cc_start: 0.8651 (mt) cc_final: 0.8421 (mt) REVERT: K 930 VAL cc_start: 0.6474 (m) cc_final: 0.5947 (m) REVERT: K 1014 MET cc_start: 0.2486 (tpp) cc_final: 0.0586 (pmm) REVERT: K 1030 PHE cc_start: 0.8184 (p90) cc_final: 0.7854 (p90) REVERT: K 1041 THR cc_start: 0.7535 (p) cc_final: 0.7196 (t) REVERT: K 1102 ARG cc_start: 0.9216 (ttt90) cc_final: 0.8460 (mpt180) REVERT: L 74 HIS cc_start: 0.8084 (t-170) cc_final: 0.7676 (t-170) REVERT: L 88 GLN cc_start: 0.8612 (mt0) cc_final: 0.8289 (tt0) REVERT: L 101 TYR cc_start: 0.8354 (m-10) cc_final: 0.7867 (m-10) REVERT: L 123 HIS cc_start: 0.8921 (t-90) cc_final: 0.7457 (t-90) REVERT: L 240 MET cc_start: 0.7976 (mtt) cc_final: 0.7627 (mtp) REVERT: L 244 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8062 (ttpt) REVERT: L 270 TRP cc_start: 0.6294 (m100) cc_final: 0.5926 (m100) REVERT: L 304 LEU cc_start: 0.9431 (tt) cc_final: 0.9212 (tp) REVERT: L 382 MET cc_start: 0.7228 (mtm) cc_final: 0.6820 (mtt) REVERT: L 388 ASP cc_start: 0.7895 (t70) cc_final: 0.7618 (t0) REVERT: L 409 SER cc_start: 0.7681 (m) cc_final: 0.7406 (m) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.7859 time to fit residues: 565.5055 Evaluate side-chains 442 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 973 ASN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 22266 Z= 0.260 Angle : 0.656 10.630 31343 Z= 0.389 Chirality : 0.052 1.616 3543 Planarity : 0.005 0.067 2998 Dihedral : 26.331 173.536 5366 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.19), residues: 1922 helix: 0.27 (0.20), residues: 629 sheet: -0.48 (0.25), residues: 456 loop : -1.47 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 203 HIS 0.005 0.001 HIS F 76 PHE 0.038 0.002 PHE K1007 TYR 0.017 0.002 TYR H 41 ARG 0.018 0.001 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7255 (mmm160) REVERT: A 57 LYS cc_start: 0.9510 (tttt) cc_final: 0.9233 (tppt) REVERT: A 70 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8006 (mtm110) REVERT: A 98 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7811 (mm-30) REVERT: A 106 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8174 (tp30) REVERT: B 37 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8880 (mtm180) REVERT: B 53 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8110 (tm-30) REVERT: C 37 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9093 (ttmm) REVERT: C 42 GLU cc_start: 0.8397 (mp0) cc_final: 0.7929 (mp0) REVERT: C 69 ASN cc_start: 0.9115 (m110) cc_final: 0.8891 (m-40) REVERT: C 96 LYS cc_start: 0.8954 (tptt) cc_final: 0.8573 (tppt) REVERT: D 100 ARG cc_start: 0.8897 (mtt90) cc_final: 0.8650 (tpp80) REVERT: D 109 LYS cc_start: 0.9094 (mttt) cc_final: 0.8568 (tppp) REVERT: E 61 LEU cc_start: 0.9522 (mt) cc_final: 0.9193 (mt) REVERT: E 98 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8023 (pp20) REVERT: E 121 MET cc_start: 0.8247 (mtt) cc_final: 0.7975 (mtm) REVERT: F 75 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8905 (tt0) REVERT: G 51 TYR cc_start: 0.9198 (t80) cc_final: 0.8769 (t80) REVERT: H 48 GLN cc_start: 0.8131 (tt0) cc_final: 0.7792 (tm-30) REVERT: H 63 MET cc_start: 0.8711 (mmm) cc_final: 0.8344 (mmm) REVERT: H 96 GLN cc_start: 0.9344 (tt0) cc_final: 0.8612 (tp40) REVERT: H 101 LEU cc_start: 0.8806 (mt) cc_final: 0.8448 (mt) REVERT: H 117 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8440 (ttpt) REVERT: K 47 GLU cc_start: 0.8148 (tp30) cc_final: 0.7937 (pm20) REVERT: K 215 GLU cc_start: 0.9203 (tp30) cc_final: 0.8660 (tp30) REVERT: K 235 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8407 (tm-30) REVERT: K 343 GLN cc_start: 0.8974 (tp40) cc_final: 0.8219 (tm-30) REVERT: K 366 ASP cc_start: 0.7428 (p0) cc_final: 0.7184 (p0) REVERT: K 736 LEU cc_start: 0.8660 (mt) cc_final: 0.8341 (mt) REVERT: K 908 ASN cc_start: 0.9238 (m-40) cc_final: 0.8978 (m-40) REVERT: K 914 LEU cc_start: 0.8646 (mt) cc_final: 0.8386 (mt) REVERT: K 1014 MET cc_start: 0.2606 (tpp) cc_final: 0.0649 (pmm) REVERT: K 1041 THR cc_start: 0.7566 (p) cc_final: 0.7261 (t) REVERT: K 1069 GLU cc_start: 0.6746 (tp30) cc_final: 0.6520 (tp30) REVERT: K 1102 ARG cc_start: 0.9270 (ttt90) cc_final: 0.8487 (mpt180) REVERT: L 88 GLN cc_start: 0.8621 (mt0) cc_final: 0.8297 (tt0) REVERT: L 240 MET cc_start: 0.8118 (mtt) cc_final: 0.7857 (mtp) REVERT: L 244 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8167 (ttpt) REVERT: L 270 TRP cc_start: 0.6298 (m100) cc_final: 0.5991 (m100) REVERT: L 304 LEU cc_start: 0.9439 (tt) cc_final: 0.9186 (tp) REVERT: L 382 MET cc_start: 0.7362 (mtm) cc_final: 0.6827 (mtt) REVERT: L 388 ASP cc_start: 0.7965 (t70) cc_final: 0.7733 (t0) REVERT: L 409 SER cc_start: 0.7555 (m) cc_final: 0.7210 (m) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.8178 time to fit residues: 576.9332 Evaluate side-chains 435 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 164 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 796 GLN ** K 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 22266 Z= 0.240 Angle : 0.640 10.625 31343 Z= 0.379 Chirality : 0.051 1.608 3543 Planarity : 0.004 0.058 2998 Dihedral : 26.350 173.383 5366 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.91 (0.19), residues: 1922 helix: 0.42 (0.20), residues: 626 sheet: -0.42 (0.25), residues: 451 loop : -1.45 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 203 HIS 0.013 0.001 HIS B 76 PHE 0.021 0.002 PHE K1003 TYR 0.016 0.001 TYR H 41 ARG 0.009 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7259 (mmm160) REVERT: A 57 LYS cc_start: 0.9516 (tttt) cc_final: 0.9240 (tppt) REVERT: A 70 ARG cc_start: 0.8308 (mtm110) cc_final: 0.7983 (mtm110) REVERT: A 98 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7753 (mm-30) REVERT: A 106 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8173 (tp30) REVERT: B 37 ARG cc_start: 0.9061 (mtm-85) cc_final: 0.8852 (mtm180) REVERT: C 37 LYS cc_start: 0.9418 (ttmm) cc_final: 0.9104 (ttmm) REVERT: C 42 GLU cc_start: 0.8419 (mp0) cc_final: 0.7944 (mp0) REVERT: C 69 ASN cc_start: 0.9086 (m110) cc_final: 0.8828 (m-40) REVERT: C 96 LYS cc_start: 0.8951 (tptt) cc_final: 0.8604 (tppt) REVERT: D 100 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8582 (tpp80) REVERT: D 109 LYS cc_start: 0.9090 (mttt) cc_final: 0.8563 (tppp) REVERT: E 61 LEU cc_start: 0.9538 (mt) cc_final: 0.9169 (mt) REVERT: E 97 CYS cc_start: 0.8941 (m) cc_final: 0.8437 (t) REVERT: E 98 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7946 (pp20) REVERT: E 121 MET cc_start: 0.8247 (mtt) cc_final: 0.8040 (mtm) REVERT: F 75 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8734 (tt0) REVERT: H 48 GLN cc_start: 0.8109 (tt0) cc_final: 0.7893 (tm-30) REVERT: H 96 GLN cc_start: 0.9200 (tt0) cc_final: 0.8553 (tp40) REVERT: H 101 LEU cc_start: 0.8820 (mt) cc_final: 0.8466 (mt) REVERT: H 117 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8398 (ttpt) REVERT: K 47 GLU cc_start: 0.8123 (tp30) cc_final: 0.7917 (pm20) REVERT: K 215 GLU cc_start: 0.9217 (tp30) cc_final: 0.8659 (tp30) REVERT: K 235 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8526 (tm-30) REVERT: K 312 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7054 (tm-30) REVERT: K 343 GLN cc_start: 0.8969 (tp40) cc_final: 0.8250 (tm-30) REVERT: K 366 ASP cc_start: 0.7418 (p0) cc_final: 0.7170 (p0) REVERT: K 724 ILE cc_start: 0.7638 (tt) cc_final: 0.7265 (tt) REVERT: K 736 LEU cc_start: 0.8703 (mt) cc_final: 0.8413 (mt) REVERT: K 908 ASN cc_start: 0.9250 (m-40) cc_final: 0.9029 (m-40) REVERT: K 914 LEU cc_start: 0.8711 (mt) cc_final: 0.8346 (mt) REVERT: K 921 ILE cc_start: 0.7605 (mp) cc_final: 0.7387 (pt) REVERT: K 1014 MET cc_start: 0.2666 (tpp) cc_final: 0.0702 (pmm) REVERT: K 1041 THR cc_start: 0.7611 (p) cc_final: 0.7231 (t) REVERT: K 1102 ARG cc_start: 0.9270 (ttt90) cc_final: 0.8448 (mpt180) REVERT: L 88 GLN cc_start: 0.8617 (mt0) cc_final: 0.8302 (tt0) REVERT: L 119 TRP cc_start: 0.8009 (m100) cc_final: 0.7140 (m100) REVERT: L 240 MET cc_start: 0.8238 (mtt) cc_final: 0.7971 (mtp) REVERT: L 244 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8140 (ttpt) REVERT: L 270 TRP cc_start: 0.6282 (m100) cc_final: 0.6065 (m100) REVERT: L 304 LEU cc_start: 0.9398 (tt) cc_final: 0.9144 (tp) REVERT: L 378 ASN cc_start: 0.9263 (m-40) cc_final: 0.9055 (m-40) REVERT: L 382 MET cc_start: 0.7388 (mtm) cc_final: 0.6787 (mtt) REVERT: L 388 ASP cc_start: 0.7888 (t70) cc_final: 0.7674 (t0) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.8118 time to fit residues: 567.3785 Evaluate side-chains 432 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 176 optimal weight: 0.3980 chunk 184 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 727 GLN ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1049 ASN L 274 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 22266 Z= 0.294 Angle : 0.674 10.566 31343 Z= 0.401 Chirality : 0.053 1.600 3543 Planarity : 0.005 0.048 2998 Dihedral : 26.451 173.889 5366 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.12 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.19 (0.19), residues: 1922 helix: 0.14 (0.20), residues: 625 sheet: -0.55 (0.25), residues: 451 loop : -1.58 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 203 HIS 0.010 0.001 HIS B 76 PHE 0.019 0.002 PHE K1003 TYR 0.017 0.002 TYR H 41 ARG 0.010 0.001 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7276 (mmm160) REVERT: A 57 LYS cc_start: 0.9516 (tttt) cc_final: 0.9252 (tppt) REVERT: A 70 ARG cc_start: 0.8329 (mtm110) cc_final: 0.8019 (mtm110) REVERT: A 94 GLN cc_start: 0.9305 (tt0) cc_final: 0.8850 (tt0) REVERT: A 98 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 106 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8187 (tp30) REVERT: C 37 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9262 (ttmm) REVERT: C 42 GLU cc_start: 0.8424 (mp0) cc_final: 0.7929 (mp0) REVERT: C 69 ASN cc_start: 0.9103 (m110) cc_final: 0.8891 (m-40) REVERT: C 96 LYS cc_start: 0.8975 (tptt) cc_final: 0.8646 (tppt) REVERT: D 100 ARG cc_start: 0.8854 (mtt90) cc_final: 0.8586 (tpp80) REVERT: D 109 LYS cc_start: 0.9138 (mttt) cc_final: 0.8621 (tppp) REVERT: E 61 LEU cc_start: 0.9542 (mt) cc_final: 0.9203 (mt) REVERT: E 98 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8036 (pp20) REVERT: F 75 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8776 (tt0) REVERT: H 63 MET cc_start: 0.8656 (mmm) cc_final: 0.8280 (mmm) REVERT: H 101 LEU cc_start: 0.8883 (mt) cc_final: 0.8545 (mt) REVERT: H 117 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8397 (ttpt) REVERT: K 114 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8381 (mmm-85) REVERT: K 158 ARG cc_start: 0.7384 (ttt180) cc_final: 0.6713 (ttm170) REVERT: K 166 ASP cc_start: 0.7669 (m-30) cc_final: 0.7330 (m-30) REVERT: K 215 GLU cc_start: 0.9240 (tp30) cc_final: 0.8677 (tp30) REVERT: K 235 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8480 (tm-30) REVERT: K 343 GLN cc_start: 0.8992 (tp40) cc_final: 0.8243 (tm-30) REVERT: K 366 ASP cc_start: 0.7424 (p0) cc_final: 0.7192 (p0) REVERT: K 736 LEU cc_start: 0.8742 (mt) cc_final: 0.8448 (mt) REVERT: K 816 LEU cc_start: 0.8592 (tp) cc_final: 0.8390 (tp) REVERT: K 908 ASN cc_start: 0.9203 (m-40) cc_final: 0.8956 (m-40) REVERT: K 914 LEU cc_start: 0.8787 (mt) cc_final: 0.8423 (mt) REVERT: K 921 ILE cc_start: 0.7574 (mp) cc_final: 0.7330 (pt) REVERT: K 1014 MET cc_start: 0.2805 (tpp) cc_final: 0.0784 (pmm) REVERT: K 1030 PHE cc_start: 0.8115 (p90) cc_final: 0.7799 (p90) REVERT: K 1041 THR cc_start: 0.7657 (p) cc_final: 0.7384 (t) REVERT: K 1102 ARG cc_start: 0.9292 (ttt90) cc_final: 0.8474 (mpt180) REVERT: L 88 GLN cc_start: 0.8674 (mt0) cc_final: 0.8347 (tt0) REVERT: L 119 TRP cc_start: 0.8057 (m100) cc_final: 0.7373 (m100) REVERT: L 244 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8223 (ttpt) REVERT: L 287 HIS cc_start: 0.8163 (m-70) cc_final: 0.7909 (m-70) REVERT: L 382 MET cc_start: 0.7497 (mtm) cc_final: 0.6866 (mtt) REVERT: L 409 SER cc_start: 0.7611 (m) cc_final: 0.7400 (m) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.8153 time to fit residues: 583.1652 Evaluate side-chains 435 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22266 Z= 0.205 Angle : 0.623 10.555 31343 Z= 0.369 Chirality : 0.050 1.612 3543 Planarity : 0.004 0.039 2998 Dihedral : 26.422 173.334 5366 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.80 (0.19), residues: 1922 helix: 0.65 (0.21), residues: 626 sheet: -0.46 (0.25), residues: 450 loop : -1.45 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 203 HIS 0.007 0.001 HIS B 76 PHE 0.014 0.001 PHE A 105 TYR 0.014 0.001 TYR H 41 ARG 0.008 0.000 ARG L 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7254 (mmm160) REVERT: A 57 LYS cc_start: 0.9493 (tttt) cc_final: 0.9234 (tppt) REVERT: A 70 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7937 (mtm110) REVERT: A 94 GLN cc_start: 0.9252 (tt0) cc_final: 0.8770 (tt0) REVERT: A 98 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7703 (mm-30) REVERT: A 106 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8126 (tp30) REVERT: C 42 GLU cc_start: 0.8366 (mp0) cc_final: 0.7884 (mp0) REVERT: C 43 ARG cc_start: 0.8425 (mtt180) cc_final: 0.8184 (mtt180) REVERT: C 69 ASN cc_start: 0.9084 (m110) cc_final: 0.8830 (m-40) REVERT: C 96 LYS cc_start: 0.8960 (tptt) cc_final: 0.8606 (tppt) REVERT: C 100 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8146 (mmp80) REVERT: D 109 LYS cc_start: 0.9092 (mttt) cc_final: 0.8544 (tppp) REVERT: E 61 LEU cc_start: 0.9554 (mt) cc_final: 0.9190 (mt) REVERT: E 97 CYS cc_start: 0.8816 (m) cc_final: 0.8437 (t) REVERT: E 98 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8028 (pp20) REVERT: F 75 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8712 (tt0) REVERT: H 63 MET cc_start: 0.8621 (mmm) cc_final: 0.8284 (mmm) REVERT: H 101 LEU cc_start: 0.8859 (mt) cc_final: 0.8490 (mt) REVERT: H 117 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8360 (ttpt) REVERT: K 166 ASP cc_start: 0.7644 (m-30) cc_final: 0.7402 (m-30) REVERT: K 204 LYS cc_start: 0.9362 (tttt) cc_final: 0.8969 (tppt) REVERT: K 215 GLU cc_start: 0.9257 (tp30) cc_final: 0.8590 (tp30) REVERT: K 343 GLN cc_start: 0.8960 (tp40) cc_final: 0.8225 (tm-30) REVERT: K 736 LEU cc_start: 0.8750 (mt) cc_final: 0.8430 (mt) REVERT: K 908 ASN cc_start: 0.9151 (m-40) cc_final: 0.8855 (m-40) REVERT: K 914 LEU cc_start: 0.8763 (mt) cc_final: 0.8411 (mt) REVERT: K 921 ILE cc_start: 0.7540 (mp) cc_final: 0.7280 (pt) REVERT: K 949 PHE cc_start: 0.8078 (p90) cc_final: 0.7426 (p90) REVERT: K 954 MET cc_start: 0.6445 (mmm) cc_final: 0.6037 (mmm) REVERT: K 990 GLN cc_start: 0.8708 (mt0) cc_final: 0.8507 (mt0) REVERT: K 1014 MET cc_start: 0.2733 (tpp) cc_final: 0.0731 (pmm) REVERT: K 1030 PHE cc_start: 0.7976 (p90) cc_final: 0.7711 (p90) REVERT: K 1102 ARG cc_start: 0.9311 (ttt90) cc_final: 0.8477 (mpt180) REVERT: L 88 GLN cc_start: 0.8656 (mt0) cc_final: 0.8309 (tt0) REVERT: L 119 TRP cc_start: 0.8039 (m100) cc_final: 0.7163 (m100) REVERT: L 270 TRP cc_start: 0.6211 (m100) cc_final: 0.5869 (m100) REVERT: L 382 MET cc_start: 0.7532 (mtm) cc_final: 0.6830 (mtt) REVERT: L 421 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6930 (tm-30) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.8137 time to fit residues: 576.0901 Evaluate side-chains 430 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113205 restraints weight = 122258.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118981 restraints weight = 50749.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122510 restraints weight = 26843.253| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22266 Z= 0.214 Angle : 0.623 10.571 31343 Z= 0.369 Chirality : 0.051 1.627 3543 Planarity : 0.004 0.061 2998 Dihedral : 26.417 173.513 5366 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.72 (0.19), residues: 1922 helix: 0.77 (0.21), residues: 627 sheet: -0.37 (0.25), residues: 444 loop : -1.47 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 83 HIS 0.009 0.001 HIS L 74 PHE 0.020 0.002 PHE K 169 TYR 0.018 0.001 TYR K 193 ARG 0.008 0.000 ARG D 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11949.59 seconds wall clock time: 216 minutes 14.15 seconds (12974.15 seconds total)