Starting phenix.real_space_refine on Sun Mar 24 07:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r91_4765/03_2024/6r91_4765_trim_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 67 5.16 5 C 12664 2.51 5 N 3870 2.21 5 O 4588 1.98 5 H 19063 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K GLU 90": "OE1" <-> "OE2" 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 146": "OD1" <-> "OD2" Residue "K GLU 160": "OE1" <-> "OE2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 307": "OE1" <-> "OE2" Residue "K ASP 318": "OD1" <-> "OD2" Residue "K ASP 339": "OD1" <-> "OD2" Residue "K GLU 351": "OE1" <-> "OE2" Residue "K ASP 366": "OD1" <-> "OD2" Residue "K GLU 368": "OE1" <-> "OE2" Residue "K ASP 744": "OD1" <-> "OD2" Residue "K PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 787": "OE1" <-> "OE2" Residue "K GLU 840": "OE1" <-> "OE2" Residue "K GLU 863": "OE1" <-> "OE2" Residue "K GLU 896": "OE1" <-> "OE2" Residue "K GLU 898": "OE1" <-> "OE2" Residue "K GLU 939": "OE1" <-> "OE2" Residue "K GLU 944": "OE1" <-> "OE2" Residue "K GLU 958": "OE1" <-> "OE2" Residue "K ASP 961": "OD1" <-> "OD2" Residue "K ASP 962": "OD1" <-> "OD2" Residue "K ASP 963": "OD1" <-> "OD2" Residue "K GLU 987": "OE1" <-> "OE2" Residue "K GLU 988": "OE1" <-> "OE2" Residue "K PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 1090": "OD1" <-> "OD2" Residue "K GLU 1107": "OE1" <-> "OE2" Residue "K GLU 1123": "OE1" <-> "OE2" Residue "K ASP 1127": "OD1" <-> "OD2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 172": "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 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 264": "OD1" <-> "OD2" 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 358": "OD1" <-> "OD2" Residue "L TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 376": "OD1" <-> "OD2" Residue "L GLU 390": "OE1" <-> "OE2" Residue "L TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40540 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1331 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1762 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1649 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1784 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: 12902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12902 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5760 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 344} Time building chain proxies: 17.55, per 1000 atoms: 0.43 Number of scatterers: 40540 At special positions: 0 Unit cell: (134.16, 184.04, 144.48, 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 67 16.00 P 288 15.00 O 4588 8.00 N 3870 7.00 C 12664 6.00 H 19063 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: 34.14 Conformation dependent library (CDL) restraints added in 3.6 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 23 sheets defined 30.0% alpha, 21.7% beta 139 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 24.85 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.691A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 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 77 removed outlier: 3.823A pdb=" N TYR B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU B 53 " --> pdb=" O LEU B 50 " (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 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.285A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 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 124 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 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.907A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.256A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 89 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 124 Processing helix chain 'K' and resid 251 through 255 removed outlier: 3.851A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 384 No H-bonds generated for 'chain 'K' and resid 382 through 384' 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 986 through 990 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: 3.687A pdb=" N PHE K1097 " --> pdb=" O LEU K1093 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU K1098 " --> pdb=" O ILE K1094 " (cutoff:3.500A) removed outlier: 4.331A 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: 3.687A pdb=" N ARG K1138 " --> pdb=" O GLU K1134 " (cutoff:3.500A) removed outlier: 4.127A 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: 4.134A 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: 7.287A pdb=" N ASN K 4 " --> pdb=" O ILE K1089 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.523A pdb=" N GLY K 17 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 6.111A 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: 6.736A pdb=" N LEU K 80 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET K 64 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE K 78 " --> pdb=" O MET K 64 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU K 66 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU K 76 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.464A 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: 3.772A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 6.266A 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: 6.892A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET K 282 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU K 304 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU K 284 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL K 302 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU K 286 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 6.340A 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 316 removed outlier: 5.658A pdb=" N LYS K 335 " --> pdb=" O ALA K 349 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA K 349 " --> pdb=" O LYS K 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 362 through 365 Processing sheet with id= K, first strand: chain 'K' and resid 749 through 751 removed outlier: 6.720A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER K 762 " --> pdb=" O ALA K 804 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLN K 806 " --> pdb=" O SER K 762 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER K 764 " --> pdb=" O GLN K 806 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.657A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 870 through 876 removed outlier: 6.834A pdb=" N SER K 883 " --> pdb=" O TYR K 871 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET K 873 " --> pdb=" O LEU K 881 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU K 881 " --> pdb=" O MET K 873 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU K 875 " --> pdb=" O LYS K 879 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS K 879 " --> pdb=" O GLU K 875 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU K 892 " --> pdb=" O THR K 901 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N THR K 901 " --> pdb=" O GLU K 892 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 911 through 917 removed outlier: 7.009A pdb=" N GLY K 924 " --> pdb=" O LEU K 912 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU K 914 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU K 922 " --> pdb=" O LEU K 914 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N THR K 916 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE K 920 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS K 936 " --> pdb=" O PHE K 942 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE K 942 " --> pdb=" O LYS K 936 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 954 through 959 removed outlier: 6.851A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE K 959 " --> pdb=" O ASN K 964 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASN K 964 " --> pdb=" O ILE K 959 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.481A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (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: 6.603A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.001A 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 229 Processing sheet with id= U, first strand: chain 'L' and resid 283 through 286 removed outlier: 4.656A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.795A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 350 through 354 removed outlier: 5.421A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 19.85 Time building geometry restraints manager: 34.76 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: 19036 1.03 - 1.22: 132 1.22 - 1.42: 9569 1.42 - 1.62: 12689 1.62 - 1.82: 111 Bond restraints: 41537 Sorted by residual: bond pdb=" C TYR L 356 " pdb=" N PRO L 357 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.27e-02 6.20e+03 5.30e+00 bond pdb=" C1' DC I 87 " pdb=" N1 DC I 87 " ideal model delta sigma weight residual 1.490 1.559 -0.069 3.00e-02 1.11e+03 5.29e+00 bond pdb=" C1' DT I 65 " pdb=" N1 DT I 65 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.29e+00 bond pdb=" C1' DC J 69 " pdb=" N1 DC J 69 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.92e+00 bond pdb=" C1' DT J 119 " pdb=" N1 DT J 119 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.86e+00 ... (remaining 41532 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.72: 1936 105.72 - 113.58: 47717 113.58 - 121.44: 17170 121.44 - 129.30: 8138 129.30 - 137.17: 256 Bond angle restraints: 75217 Sorted by residual: angle pdb=" CA LEU C 116 " pdb=" CB LEU C 116 " pdb=" CG LEU C 116 " ideal model delta sigma weight residual 116.30 137.17 -20.87 3.50e+00 8.16e-02 3.55e+01 angle pdb=" N GLY D 105 " pdb=" CA GLY D 105 " pdb=" C GLY D 105 " ideal model delta sigma weight residual 113.18 126.60 -13.42 2.37e+00 1.78e-01 3.21e+01 angle pdb=" N GLY H 105 " pdb=" CA GLY H 105 " pdb=" C GLY H 105 " ideal model delta sigma weight residual 113.18 126.59 -13.41 2.37e+00 1.78e-01 3.20e+01 angle pdb=" C THR E 81 " pdb=" N ASP E 82 " pdb=" CA ASP E 82 " ideal model delta sigma weight residual 122.08 129.19 -7.11 1.47e+00 4.63e-01 2.34e+01 angle pdb=" N ARG E 132 " pdb=" CA ARG E 132 " pdb=" CB ARG E 132 " ideal model delta sigma weight residual 110.39 118.21 -7.82 1.66e+00 3.63e-01 2.22e+01 ... (remaining 75212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 16485 34.94 - 69.88: 1847 69.88 - 104.82: 50 104.82 - 139.76: 0 139.76 - 174.70: 3 Dihedral angle restraints: 18385 sinusoidal: 11897 harmonic: 6488 Sorted by residual: 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 -124.02 -55.98 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO L 64 " pdb=" C PRO L 64 " pdb=" N PRO L 65 " pdb=" CA PRO L 65 " ideal model delta harmonic sigma weight residual 180.00 -140.72 -39.28 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA CYS L 66 " pdb=" C CYS L 66 " pdb=" N ARG L 67 " pdb=" CA ARG L 67 " ideal model delta harmonic sigma weight residual 180.00 150.48 29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 18382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2867 0.065 - 0.129: 610 0.129 - 0.194: 81 0.194 - 0.258: 10 0.258 - 0.323: 1 Chirality restraints: 3569 Sorted by residual: chirality pdb=" CG LEU L 324 " pdb=" CB LEU L 324 " pdb=" CD1 LEU L 324 " pdb=" CD2 LEU L 324 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ARG A 132 " pdb=" N ARG A 132 " pdb=" C ARG A 132 " pdb=" CB ARG A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LEU C 116 " pdb=" N LEU C 116 " pdb=" C LEU C 116 " pdb=" CB LEU C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3566 not shown) Planarity restraints: 5124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 65 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C ASN F 65 " -0.087 2.00e-02 2.50e+03 pdb=" O ASN F 65 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL F 66 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 65 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C ASN B 65 " 0.078 2.00e-02 2.50e+03 pdb=" O ASN B 65 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL B 66 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 64 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C GLU B 64 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 64 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN B 65 " -0.025 2.00e-02 2.50e+03 ... (remaining 5121 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1823 2.18 - 2.79: 73991 2.79 - 3.39: 108849 3.39 - 4.00: 149123 4.00 - 4.60: 221658 Nonbonded interactions: 555444 Sorted by model distance: nonbonded pdb=" H ASP K 925 " pdb=" O SER K 929 " model vdw 1.578 1.850 nonbonded pdb="HH22 ARG A 41 " pdb=" O3' DT J 85 " model vdw 1.611 1.850 nonbonded pdb="HH12 ARG A 73 " pdb=" OP1 DC I 47 " model vdw 1.647 1.850 nonbonded pdb=" O CYS L 66 " pdb="HE22 GLN L 92 " model vdw 1.649 1.850 nonbonded pdb=" O LYS F 60 " pdb=" H GLU F 64 " model vdw 1.654 1.850 ... (remaining 555439 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' and resid 39 through 136) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 24 through 28 or (resid 29 and (name N or name CA or name C or name O \ or name HA2 or name HA3)) or resid 30 through 103)) } ncs_group { reference = chain 'C' selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 12 through 120)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 96 or resid 99 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: 0.400 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: 0.540 Extract box with map and model: 4.080 Check model and map are aligned: 0.670 Set scattering table: 0.390 Process input model: 148.660 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 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 : 0.006 0.069 22474 Z= 0.377 Angle : 1.014 20.866 31615 Z= 0.595 Chirality : 0.053 0.323 3569 Planarity : 0.007 0.075 3037 Dihedral : 23.872 174.700 9214 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.57 % Favored : 94.97 % Rotamer: Outliers : 0.65 % Allowed : 3.21 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -0.83 (0.17), residues: 1947 helix: 0.61 (0.18), residues: 630 sheet: -0.33 (0.23), residues: 476 loop : -1.55 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP K 207 HIS 0.011 0.002 HIS K 991 PHE 0.045 0.003 PHE K 949 TYR 0.031 0.004 TYR K 171 ARG 0.027 0.002 ARG K 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 458 time to evaluate : 2.212 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: A 56 GLN cc_start: 0.9015 (mt0) cc_final: 0.8585 (mt0) REVERT: A 57 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7611 (mmtm) REVERT: A 59 THR cc_start: 0.6750 (p) cc_final: 0.6367 (p) REVERT: A 62 LEU cc_start: 0.8471 (mt) cc_final: 0.8237 (mm) REVERT: A 119 THR cc_start: 0.8326 (m) cc_final: 0.7906 (p) REVERT: B 26 ASN cc_start: 0.7926 (m110) cc_final: 0.7580 (m110) REVERT: C 37 LYS cc_start: 0.5886 (mttm) cc_final: 0.5580 (tmtt) REVERT: C 73 ASP cc_start: 0.8913 (t0) cc_final: 0.8660 (t0) REVERT: C 102 THR cc_start: 0.8035 (m) cc_final: 0.7359 (p) REVERT: D 40 ILE cc_start: 0.7702 (tp) cc_final: 0.7167 (pt) REVERT: D 72 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4911 (tt0) REVERT: D 86 LYS cc_start: 0.8977 (tptt) cc_final: 0.8729 (tppp) REVERT: D 117 LYS cc_start: 0.8450 (tmtt) cc_final: 0.7884 (ttmt) REVERT: E 54 ARG cc_start: 0.6327 (ttp-170) cc_final: 0.6118 (ttp-110) REVERT: E 77 GLN cc_start: 0.8902 (tt0) cc_final: 0.8382 (tp40) REVERT: E 91 MET cc_start: 0.6204 (mmm) cc_final: 0.5584 (mmm) REVERT: E 94 GLN cc_start: 0.7609 (tt0) cc_final: 0.6509 (tp40) REVERT: E 95 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7973 (mm-30) REVERT: E 98 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7796 (tm-30) REVERT: E 119 THR cc_start: 0.7762 (m) cc_final: 0.7556 (p) REVERT: G 31 VAL cc_start: 0.7147 (t) cc_final: 0.6946 (p) REVERT: G 63 ILE cc_start: 0.5900 (mm) cc_final: 0.5544 (tp) REVERT: H 36 GLU cc_start: 0.6574 (pp20) cc_final: 0.5840 (pt0) REVERT: H 106 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7339 (mp0) REVERT: K 7 VAL cc_start: 0.8352 (p) cc_final: 0.7188 (p) REVERT: K 151 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7936 (mm-30) REVERT: K 166 ASP cc_start: 0.7170 (t0) cc_final: 0.6561 (t0) REVERT: K 202 PHE cc_start: 0.3629 (m-80) cc_final: 0.3323 (m-10) REVERT: K 218 MET cc_start: 0.8006 (mtm) cc_final: 0.6297 (tpp) REVERT: K 258 ILE cc_start: 0.8298 (mt) cc_final: 0.8022 (mt) REVERT: K 713 ARG cc_start: 0.3651 (ttt180) cc_final: 0.3210 (mmt180) REVERT: K 840 GLU cc_start: 0.6311 (tp30) cc_final: 0.5728 (tp30) REVERT: K 873 MET cc_start: 0.4709 (mtm) cc_final: 0.3896 (mpp) REVERT: K 897 LYS cc_start: 0.9234 (mttt) cc_final: 0.8908 (mtpt) REVERT: K 908 ASN cc_start: 0.6647 (m-40) cc_final: 0.6392 (p0) REVERT: K 989 ARG cc_start: 0.4048 (mtm-85) cc_final: 0.3845 (mtm-85) REVERT: K 1092 ASP cc_start: 0.7161 (m-30) cc_final: 0.6851 (p0) REVERT: L 123 HIS cc_start: 0.7004 (t-90) cc_final: 0.6274 (m170) REVERT: L 135 ASP cc_start: 0.3387 (m-30) cc_final: 0.2581 (m-30) REVERT: L 187 LYS cc_start: 0.9302 (mttm) cc_final: 0.9078 (mmmt) REVERT: L 214 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7521 (mtp-110) REVERT: L 270 TRP cc_start: 0.7125 (m100) cc_final: 0.6442 (m100) REVERT: L 299 ASP cc_start: 0.6924 (t0) cc_final: 0.6600 (t0) REVERT: L 356 TYR cc_start: 0.8174 (t80) cc_final: 0.7737 (t80) REVERT: L 403 MET cc_start: 0.8117 (tpt) cc_final: 0.7514 (tpt) REVERT: L 424 ARG cc_start: 0.6479 (mtm180) cc_final: 0.6121 (ptp-170) outliers start: 11 outliers final: 2 residues processed: 465 average time/residue: 0.8647 time to fit residues: 572.9230 Evaluate side-chains 333 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 330 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 26 ASN B 94 GLN D 68 ASN D 96 GLN E 69 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN G 25 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN K 319 ASN ** K 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 845 GLN K 877 ASN K1034 ASN K1059 ASN L 91 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 22474 Z= 0.284 Angle : 0.700 6.925 31615 Z= 0.416 Chirality : 0.044 0.167 3569 Planarity : 0.006 0.053 3037 Dihedral : 27.175 178.242 5404 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % 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: -0.44 (0.18), residues: 1947 helix: 1.02 (0.20), residues: 638 sheet: -0.14 (0.24), residues: 445 loop : -1.37 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 236 HIS 0.010 0.002 HIS K 789 PHE 0.017 0.002 PHE A 68 TYR 0.021 0.002 TYR K 42 ARG 0.009 0.001 ARG K 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 378 time to evaluate : 2.633 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: A 56 GLN cc_start: 0.9357 (mt0) cc_final: 0.9020 (mt0) REVERT: A 57 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7696 (mmtm) REVERT: A 97 CYS cc_start: 0.9628 (m) cc_final: 0.9325 (m) REVERT: A 98 GLU cc_start: 0.8705 (pp20) cc_final: 0.8389 (pp20) REVERT: B 94 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6896 (tp40) REVERT: C 37 LYS cc_start: 0.5974 (mttm) cc_final: 0.5700 (tmtt) REVERT: C 62 GLU cc_start: 0.8007 (tt0) cc_final: 0.7799 (mt-10) REVERT: C 73 ASP cc_start: 0.8900 (t0) cc_final: 0.8626 (t0) REVERT: D 36 GLU cc_start: 0.7229 (pp20) cc_final: 0.6408 (pp20) REVERT: D 40 ILE cc_start: 0.7852 (tp) cc_final: 0.7283 (pt) REVERT: D 86 LYS cc_start: 0.9042 (tptt) cc_final: 0.8678 (tppp) REVERT: D 117 LYS cc_start: 0.8604 (tmtt) cc_final: 0.8164 (ttmt) REVERT: E 56 GLN cc_start: 0.9174 (mt0) cc_final: 0.8967 (mt0) REVERT: E 77 GLN cc_start: 0.8965 (tt0) cc_final: 0.8429 (tp40) REVERT: E 91 MET cc_start: 0.6353 (mmm) cc_final: 0.5838 (tpt) REVERT: E 94 GLN cc_start: 0.7618 (tt0) cc_final: 0.6605 (tp40) REVERT: G 31 VAL cc_start: 0.7203 (t) cc_final: 0.6992 (m) REVERT: G 63 ILE cc_start: 0.6109 (mm) cc_final: 0.5761 (tp) REVERT: G 65 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6343 (mm-30) REVERT: H 36 GLU cc_start: 0.6877 (pp20) cc_final: 0.6633 (pp20) REVERT: K 7 VAL cc_start: 0.8854 (p) cc_final: 0.8471 (p) REVERT: K 151 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8051 (mm-30) REVERT: K 164 VAL cc_start: 0.7740 (t) cc_final: 0.7451 (t) REVERT: K 180 PHE cc_start: 0.4218 (p90) cc_final: 0.3919 (p90) REVERT: K 218 MET cc_start: 0.8112 (mtm) cc_final: 0.6615 (tpp) REVERT: K 244 LYS cc_start: 0.6303 (mmmt) cc_final: 0.6091 (tptp) REVERT: K 713 ARG cc_start: 0.3554 (ttt180) cc_final: 0.3192 (mmt180) REVERT: K 840 GLU cc_start: 0.6471 (tp30) cc_final: 0.6018 (tp30) REVERT: K 844 LYS cc_start: 0.7161 (mmtm) cc_final: 0.6812 (mtmt) REVERT: K 873 MET cc_start: 0.4723 (mtm) cc_final: 0.3532 (mpp) REVERT: K 908 ASN cc_start: 0.5592 (m-40) cc_final: 0.5239 (p0) REVERT: K 1072 PHE cc_start: 0.7148 (t80) cc_final: 0.5454 (m-10) REVERT: L 77 LYS cc_start: 0.6895 (mtpt) cc_final: 0.6533 (mttm) REVERT: L 123 HIS cc_start: 0.7089 (t-90) cc_final: 0.6141 (m170) REVERT: L 125 SER cc_start: 0.7113 (m) cc_final: 0.6721 (m) REVERT: L 177 MET cc_start: 0.7866 (tpp) cc_final: 0.7510 (tpp) REVERT: L 214 ARG cc_start: 0.8338 (mtt90) cc_final: 0.7574 (mtp-110) REVERT: L 215 MET cc_start: 0.7168 (mtm) cc_final: 0.6946 (mtm) REVERT: L 270 TRP cc_start: 0.7149 (m100) cc_final: 0.5041 (m100) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.8024 time to fit residues: 446.7228 Evaluate side-chains 315 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 55 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 217 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN L 92 GLN L 274 GLN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22474 Z= 0.191 Angle : 0.614 5.983 31615 Z= 0.368 Chirality : 0.041 0.166 3569 Planarity : 0.004 0.053 3037 Dihedral : 27.159 176.554 5404 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.06 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.15 (0.19), residues: 1947 helix: 1.35 (0.20), residues: 641 sheet: -0.20 (0.24), residues: 459 loop : -1.14 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 207 HIS 0.004 0.001 HIS B 76 PHE 0.020 0.001 PHE K1030 TYR 0.014 0.001 TYR D 41 ARG 0.007 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.338 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: A 56 GLN cc_start: 0.9239 (mt0) cc_final: 0.8832 (mt0) REVERT: A 57 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7681 (mmtm) REVERT: A 93 LEU cc_start: 0.8845 (tt) cc_final: 0.8565 (tt) REVERT: A 97 CYS cc_start: 0.9627 (m) cc_final: 0.9341 (m) REVERT: A 98 GLU cc_start: 0.8790 (pp20) cc_final: 0.8526 (pp20) REVERT: C 37 LYS cc_start: 0.6098 (mttm) cc_final: 0.5683 (tmtt) REVERT: C 62 GLU cc_start: 0.7634 (tt0) cc_final: 0.7412 (mt-10) REVERT: C 73 ASP cc_start: 0.8826 (t0) cc_final: 0.8562 (t0) REVERT: D 40 ILE cc_start: 0.8276 (tp) cc_final: 0.7702 (pt) REVERT: D 86 LYS cc_start: 0.9028 (tptt) cc_final: 0.8686 (tppp) REVERT: D 117 LYS cc_start: 0.8573 (tmtt) cc_final: 0.8102 (ttmt) REVERT: E 56 GLN cc_start: 0.9266 (mt0) cc_final: 0.9038 (mt0) REVERT: E 77 GLN cc_start: 0.8504 (tt0) cc_final: 0.7835 (tp40) REVERT: E 91 MET cc_start: 0.6238 (mmm) cc_final: 0.5521 (tpt) REVERT: E 95 GLU cc_start: 0.8785 (mm-30) cc_final: 0.7873 (mm-30) REVERT: G 63 ILE cc_start: 0.6285 (mm) cc_final: 0.5995 (tp) REVERT: H 36 GLU cc_start: 0.6918 (pp20) cc_final: 0.6413 (pt0) REVERT: K 7 VAL cc_start: 0.8671 (p) cc_final: 0.8323 (p) REVERT: K 151 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8098 (mm-30) REVERT: K 164 VAL cc_start: 0.7852 (t) cc_final: 0.7607 (t) REVERT: K 202 PHE cc_start: 0.3834 (m-10) cc_final: 0.3554 (m-10) REVERT: K 218 MET cc_start: 0.7939 (mtm) cc_final: 0.6391 (tpp) REVERT: K 840 GLU cc_start: 0.5811 (tp30) cc_final: 0.5461 (tp30) REVERT: K 844 LYS cc_start: 0.7298 (mmtm) cc_final: 0.6825 (mtmt) REVERT: K 873 MET cc_start: 0.4832 (mtm) cc_final: 0.4056 (mpp) REVERT: K 897 LYS cc_start: 0.9276 (mttt) cc_final: 0.8980 (mtpt) REVERT: K 906 TYR cc_start: 0.4080 (m-80) cc_final: 0.3846 (m-80) REVERT: K 908 ASN cc_start: 0.5647 (m-40) cc_final: 0.5168 (p0) REVERT: K 910 MET cc_start: 0.5748 (ptp) cc_final: 0.5404 (pmm) REVERT: K 1072 PHE cc_start: 0.7082 (t80) cc_final: 0.5420 (m-10) REVERT: L 77 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6388 (mttm) REVERT: L 123 HIS cc_start: 0.7053 (t-90) cc_final: 0.6572 (m170) REVERT: L 126 THR cc_start: 0.6259 (m) cc_final: 0.5974 (m) REVERT: L 177 MET cc_start: 0.7825 (tpp) cc_final: 0.7043 (tpp) REVERT: L 214 ARG cc_start: 0.8422 (mtt90) cc_final: 0.7542 (mtp-110) REVERT: L 240 MET cc_start: 0.6546 (mmm) cc_final: 0.6161 (mmm) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.8098 time to fit residues: 430.2462 Evaluate side-chains 298 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 39 ASN D 64 ASN G 39 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 727 GLN ** K 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 22474 Z= 0.309 Angle : 0.695 6.753 31615 Z= 0.416 Chirality : 0.044 0.169 3569 Planarity : 0.005 0.062 3037 Dihedral : 27.170 178.170 5404 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.52 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -0.95 (0.18), residues: 1947 helix: 0.21 (0.19), residues: 640 sheet: -0.37 (0.25), residues: 446 loop : -1.36 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 207 HIS 0.013 0.002 HIS K 789 PHE 0.024 0.002 PHE B 101 TYR 0.022 0.002 TYR B 52 ARG 0.006 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.870 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: A 56 GLN cc_start: 0.9273 (mt0) cc_final: 0.8983 (mt0) REVERT: A 57 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7706 (mmtt) REVERT: A 98 GLU cc_start: 0.8857 (pp20) cc_final: 0.8515 (pp20) REVERT: C 37 LYS cc_start: 0.6154 (mttm) cc_final: 0.5717 (tmtt) REVERT: C 39 ASN cc_start: 0.7138 (m-40) cc_final: 0.6872 (m110) REVERT: C 62 GLU cc_start: 0.7441 (tt0) cc_final: 0.7098 (mt-10) REVERT: D 35 LYS cc_start: 0.6742 (tttp) cc_final: 0.6144 (pttp) REVERT: D 40 ILE cc_start: 0.8366 (tp) cc_final: 0.7808 (pt) REVERT: D 86 LYS cc_start: 0.9066 (tptt) cc_final: 0.8776 (tppp) REVERT: D 117 LYS cc_start: 0.8879 (tmtt) cc_final: 0.8450 (ttmt) REVERT: E 77 GLN cc_start: 0.8988 (tt0) cc_final: 0.8591 (tp40) REVERT: E 100 TYR cc_start: 0.7577 (t80) cc_final: 0.7130 (t80) REVERT: F 28 GLN cc_start: 0.8162 (mp10) cc_final: 0.7705 (mp10) REVERT: G 63 ILE cc_start: 0.6295 (mm) cc_final: 0.5964 (tp) REVERT: K 7 VAL cc_start: 0.8844 (p) cc_final: 0.8536 (p) REVERT: K 151 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8163 (mm-30) REVERT: K 164 VAL cc_start: 0.8194 (t) cc_final: 0.7952 (t) REVERT: K 180 PHE cc_start: 0.4757 (p90) cc_final: 0.4441 (p90) REVERT: K 218 MET cc_start: 0.8101 (mtm) cc_final: 0.6699 (tpp) REVERT: K 287 LYS cc_start: 0.5717 (mmmt) cc_final: 0.5461 (mmmt) REVERT: K 312 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7181 (tm-30) REVERT: K 840 GLU cc_start: 0.5798 (tp30) cc_final: 0.5567 (tp30) REVERT: K 844 LYS cc_start: 0.7340 (mmtm) cc_final: 0.6926 (mtmt) REVERT: K 873 MET cc_start: 0.4997 (mtm) cc_final: 0.3780 (mpp) REVERT: K 910 MET cc_start: 0.6177 (ptp) cc_final: 0.5530 (pmm) REVERT: K 1072 PHE cc_start: 0.7456 (t80) cc_final: 0.5516 (m-10) REVERT: L 214 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7757 (mtp-110) REVERT: L 215 MET cc_start: 0.6888 (mtm) cc_final: 0.6649 (mtm) REVERT: L 240 MET cc_start: 0.6427 (mmm) cc_final: 0.6111 (mmm) REVERT: L 409 SER cc_start: 0.5369 (m) cc_final: 0.4952 (m) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.8061 time to fit residues: 413.7707 Evaluate side-chains 302 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 952 ASN ** K 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 22474 Z= 0.338 Angle : 0.741 7.066 31615 Z= 0.440 Chirality : 0.045 0.183 3569 Planarity : 0.006 0.084 3037 Dihedral : 27.366 177.820 5404 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.32 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -1.69 (0.18), residues: 1947 helix: -0.60 (0.19), residues: 633 sheet: -0.49 (0.24), residues: 467 loop : -1.82 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 256 HIS 0.013 0.002 HIS K1077 PHE 0.041 0.003 PHE G 26 TYR 0.027 0.003 TYR K 812 ARG 0.009 0.001 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.656 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: A 56 GLN cc_start: 0.9385 (mt0) cc_final: 0.8980 (mt0) REVERT: A 57 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7667 (mmtm) REVERT: A 98 GLU cc_start: 0.8954 (pp20) cc_final: 0.8628 (pp20) REVERT: C 37 LYS cc_start: 0.6075 (mttm) cc_final: 0.5586 (tmtt) REVERT: C 42 GLU cc_start: 0.8131 (mp0) cc_final: 0.7699 (mp0) REVERT: C 62 GLU cc_start: 0.7435 (tt0) cc_final: 0.7050 (mt-10) REVERT: D 35 LYS cc_start: 0.6977 (tttp) cc_final: 0.6314 (pttp) REVERT: D 86 LYS cc_start: 0.9103 (tptt) cc_final: 0.8816 (tppp) REVERT: E 77 GLN cc_start: 0.9161 (tt0) cc_final: 0.8782 (tp40) REVERT: E 104 LEU cc_start: 0.9207 (tp) cc_final: 0.8971 (mt) REVERT: K 7 VAL cc_start: 0.8740 (p) cc_final: 0.8529 (p) REVERT: K 114 ARG cc_start: 0.3560 (mtp85) cc_final: 0.3232 (ttm110) REVERT: K 151 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8205 (mm-30) REVERT: K 844 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6849 (mtmt) REVERT: K 873 MET cc_start: 0.5246 (mtm) cc_final: 0.3979 (mpp) REVERT: K 910 MET cc_start: 0.5425 (ptp) cc_final: 0.4770 (pmm) REVERT: K 1014 MET cc_start: 0.3427 (tpp) cc_final: 0.1340 (mtm) REVERT: L 77 LYS cc_start: 0.6898 (mtmt) cc_final: 0.6313 (mttm) REVERT: L 214 ARG cc_start: 0.8658 (mtt90) cc_final: 0.7645 (mtp-110) REVERT: L 270 TRP cc_start: 0.6250 (m100) cc_final: 0.3644 (m100) REVERT: L 288 ARG cc_start: 0.7455 (mtt90) cc_final: 0.6756 (mtm110) REVERT: L 347 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7948 (mtm110) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.8096 time to fit residues: 416.7163 Evaluate side-chains 306 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 809 GLN ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 993 GLN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22474 Z= 0.221 Angle : 0.639 6.643 31615 Z= 0.382 Chirality : 0.042 0.161 3569 Planarity : 0.005 0.057 3037 Dihedral : 27.340 177.208 5404 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -1.31 (0.18), residues: 1947 helix: 0.03 (0.20), residues: 633 sheet: -0.53 (0.24), residues: 461 loop : -1.70 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 256 HIS 0.011 0.001 HIS K 789 PHE 0.020 0.002 PHE B 101 TYR 0.034 0.002 TYR D 84 ARG 0.006 0.000 ARG K 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.668 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: A 56 GLN cc_start: 0.9270 (mt0) cc_final: 0.8801 (mt0) REVERT: A 57 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7628 (mmtt) REVERT: A 63 ILE cc_start: 0.7682 (mm) cc_final: 0.7425 (mm) REVERT: A 98 GLU cc_start: 0.8871 (pp20) cc_final: 0.8594 (pp20) REVERT: C 42 GLU cc_start: 0.8001 (mp0) cc_final: 0.7580 (mp0) REVERT: C 62 GLU cc_start: 0.7369 (tt0) cc_final: 0.7049 (mt-10) REVERT: D 35 LYS cc_start: 0.6967 (tttp) cc_final: 0.6724 (tmmt) REVERT: D 84 TYR cc_start: 0.5754 (m-80) cc_final: 0.5439 (m-10) REVERT: D 86 LYS cc_start: 0.9121 (tptt) cc_final: 0.8736 (tppp) REVERT: D 121 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9016 (tmtt) REVERT: E 77 GLN cc_start: 0.8854 (tt0) cc_final: 0.8293 (tp40) REVERT: E 104 LEU cc_start: 0.9189 (tp) cc_final: 0.8879 (mt) REVERT: E 134 GLU cc_start: 0.5163 (tp30) cc_final: 0.4535 (tp30) REVERT: F 53 GLU cc_start: 0.8283 (pm20) cc_final: 0.8026 (pm20) REVERT: G 18 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8279 (mtp180) REVERT: H 36 GLU cc_start: 0.7084 (pp20) cc_final: 0.6699 (pt0) REVERT: K 151 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7996 (mm-30) REVERT: K 218 MET cc_start: 0.8074 (mtm) cc_final: 0.6640 (tpp) REVERT: K 814 LEU cc_start: 0.5666 (mt) cc_final: 0.5407 (mt) REVERT: K 844 LYS cc_start: 0.7197 (mmtm) cc_final: 0.6811 (mtmt) REVERT: K 873 MET cc_start: 0.5104 (mtm) cc_final: 0.3784 (mpp) REVERT: K 910 MET cc_start: 0.5836 (ptp) cc_final: 0.5374 (pmm) REVERT: K 959 ILE cc_start: 0.3235 (mt) cc_final: 0.2905 (mt) REVERT: K 1014 MET cc_start: 0.3643 (tpp) cc_final: 0.1896 (mtm) REVERT: L 77 LYS cc_start: 0.6863 (mtmt) cc_final: 0.6274 (mttm) REVERT: L 214 ARG cc_start: 0.8692 (mtt90) cc_final: 0.7977 (mtp-110) REVERT: L 270 TRP cc_start: 0.6076 (m100) cc_final: 0.3465 (m100) REVERT: L 288 ARG cc_start: 0.7422 (mtt90) cc_final: 0.6735 (mtm110) REVERT: L 347 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7727 (mtm110) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.8056 time to fit residues: 404.5449 Evaluate side-chains 306 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 120 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 ASN K1056 ASN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22474 Z= 0.206 Angle : 0.622 6.263 31615 Z= 0.372 Chirality : 0.041 0.159 3569 Planarity : 0.004 0.061 3037 Dihedral : 27.317 177.040 5404 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.16 (0.18), residues: 1947 helix: 0.35 (0.20), residues: 633 sheet: -0.56 (0.24), residues: 467 loop : -1.72 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 256 HIS 0.010 0.001 HIS K 789 PHE 0.020 0.001 PHE B 101 TYR 0.019 0.002 TYR D 84 ARG 0.007 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.980 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: A 56 GLN cc_start: 0.9275 (mt0) cc_final: 0.8705 (mt0) REVERT: A 57 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7618 (mmtm) REVERT: A 98 GLU cc_start: 0.8857 (pp20) cc_final: 0.8541 (pp20) REVERT: C 37 LYS cc_start: 0.6169 (mttm) cc_final: 0.5707 (tmtt) REVERT: C 39 ASN cc_start: 0.7913 (m110) cc_final: 0.7688 (m110) REVERT: C 42 GLU cc_start: 0.7961 (mp0) cc_final: 0.7617 (mp0) REVERT: C 62 GLU cc_start: 0.7348 (tt0) cc_final: 0.7041 (mt-10) REVERT: D 35 LYS cc_start: 0.6914 (tttp) cc_final: 0.6665 (tmmt) REVERT: D 36 GLU cc_start: 0.7414 (pp20) cc_final: 0.6620 (pp20) REVERT: D 84 TYR cc_start: 0.5732 (m-80) cc_final: 0.5432 (m-10) REVERT: D 86 LYS cc_start: 0.9125 (tptt) cc_final: 0.8817 (tppp) REVERT: D 121 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9009 (tmtt) REVERT: E 77 GLN cc_start: 0.8833 (tt0) cc_final: 0.8271 (tp40) REVERT: E 94 GLN cc_start: 0.6875 (tt0) cc_final: 0.5803 (tp40) REVERT: E 104 LEU cc_start: 0.9114 (tp) cc_final: 0.8863 (mt) REVERT: F 51 ILE cc_start: 0.8703 (mm) cc_final: 0.8466 (mm) REVERT: F 53 GLU cc_start: 0.8293 (pm20) cc_final: 0.8005 (pm20) REVERT: G 63 ILE cc_start: 0.6370 (mm) cc_final: 0.6053 (tp) REVERT: H 36 GLU cc_start: 0.7121 (pp20) cc_final: 0.6739 (pt0) REVERT: K 151 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7959 (mm-30) REVERT: K 218 MET cc_start: 0.7998 (mtm) cc_final: 0.6480 (tpp) REVERT: K 814 LEU cc_start: 0.6143 (mt) cc_final: 0.5914 (mt) REVERT: K 835 MET cc_start: 0.4929 (mmm) cc_final: 0.3974 (mmm) REVERT: K 844 LYS cc_start: 0.7233 (mmtm) cc_final: 0.6940 (mtmt) REVERT: K 873 MET cc_start: 0.5064 (mtm) cc_final: 0.3746 (mpp) REVERT: K 910 MET cc_start: 0.5844 (ptp) cc_final: 0.5370 (pmm) REVERT: K 1014 MET cc_start: 0.3769 (tpp) cc_final: 0.2202 (mtm) REVERT: L 77 LYS cc_start: 0.6983 (mtmt) cc_final: 0.6270 (mttm) REVERT: L 214 ARG cc_start: 0.8694 (mtt90) cc_final: 0.7856 (mtp-110) REVERT: L 270 TRP cc_start: 0.6038 (m100) cc_final: 0.3403 (m100) REVERT: L 288 ARG cc_start: 0.7453 (mtt90) cc_final: 0.6722 (mtm110) REVERT: L 347 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7929 (mtm110) REVERT: L 376 ASP cc_start: 0.7063 (t70) cc_final: 0.6828 (t70) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.8039 time to fit residues: 407.3538 Evaluate side-chains 305 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 135 optimal weight: 0.2980 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 22474 Z= 0.286 Angle : 0.677 6.214 31615 Z= 0.405 Chirality : 0.043 0.166 3569 Planarity : 0.005 0.058 3037 Dihedral : 27.359 177.648 5404 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.30 % Favored : 90.65 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 98.99 % 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: -1.59 (0.18), residues: 1947 helix: -0.19 (0.20), residues: 632 sheet: -0.65 (0.25), residues: 442 loop : -1.89 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 256 HIS 0.014 0.002 HIS K 789 PHE 0.025 0.002 PHE L 110 TYR 0.019 0.002 TYR B 52 ARG 0.007 0.001 ARG K 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 2.437 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: A 56 GLN cc_start: 0.9338 (mt0) cc_final: 0.8773 (mt0) REVERT: A 57 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7679 (mmtm) REVERT: A 98 GLU cc_start: 0.8971 (pp20) cc_final: 0.8578 (pp20) REVERT: C 39 ASN cc_start: 0.8134 (m-40) cc_final: 0.7864 (m110) REVERT: C 42 GLU cc_start: 0.7927 (mp0) cc_final: 0.7628 (mp0) REVERT: C 62 GLU cc_start: 0.7196 (tt0) cc_final: 0.6943 (mt-10) REVERT: D 36 GLU cc_start: 0.7353 (pp20) cc_final: 0.6295 (pp20) REVERT: D 84 TYR cc_start: 0.6413 (m-80) cc_final: 0.6122 (m-10) REVERT: D 86 LYS cc_start: 0.9139 (tptt) cc_final: 0.8818 (tppp) REVERT: D 121 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8861 (tmtt) REVERT: E 73 ARG cc_start: 0.5506 (mtt-85) cc_final: 0.5027 (mtt90) REVERT: E 77 GLN cc_start: 0.8886 (tt0) cc_final: 0.8299 (tp40) REVERT: E 94 GLN cc_start: 0.7012 (tt0) cc_final: 0.5851 (tp40) REVERT: F 53 GLU cc_start: 0.8401 (pm20) cc_final: 0.7955 (pm20) REVERT: G 18 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6667 (mtp-110) REVERT: K 111 ARG cc_start: 0.2726 (tpt170) cc_final: 0.1351 (mmt90) REVERT: K 151 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8017 (mm-30) REVERT: K 814 LEU cc_start: 0.5726 (mt) cc_final: 0.5430 (mt) REVERT: K 844 LYS cc_start: 0.7252 (mmtm) cc_final: 0.6930 (mtmt) REVERT: K 873 MET cc_start: 0.5529 (mtm) cc_final: 0.4257 (mpp) REVERT: K 910 MET cc_start: 0.5566 (ptp) cc_final: 0.4565 (pmm) REVERT: K 959 ILE cc_start: 0.3522 (mt) cc_final: 0.3196 (mt) REVERT: K 1014 MET cc_start: 0.4215 (tpp) cc_final: 0.2114 (mtm) REVERT: L 77 LYS cc_start: 0.7070 (mtmt) cc_final: 0.6343 (mttm) REVERT: L 214 ARG cc_start: 0.8741 (mtt90) cc_final: 0.7898 (mtp-110) REVERT: L 270 TRP cc_start: 0.6170 (m100) cc_final: 0.3439 (m100) REVERT: L 288 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7170 (mtm110) REVERT: L 376 ASP cc_start: 0.7116 (t70) cc_final: 0.6831 (t70) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.8601 time to fit residues: 436.9939 Evaluate side-chains 303 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22474 Z= 0.263 Angle : 0.662 7.395 31615 Z= 0.397 Chirality : 0.042 0.165 3569 Planarity : 0.005 0.056 3037 Dihedral : 27.384 177.413 5404 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % 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: -1.64 (0.18), residues: 1947 helix: -0.23 (0.20), residues: 630 sheet: -0.75 (0.25), residues: 442 loop : -1.88 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 256 HIS 0.014 0.002 HIS K 789 PHE 0.028 0.002 PHE B 101 TYR 0.017 0.002 TYR B 52 ARG 0.007 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.438 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: A 56 GLN cc_start: 0.9284 (mt0) cc_final: 0.8734 (mt0) REVERT: A 57 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7618 (mmtt) REVERT: A 98 GLU cc_start: 0.8913 (pp20) cc_final: 0.8624 (pp20) REVERT: C 37 LYS cc_start: 0.6212 (mttm) cc_final: 0.5765 (tmtt) REVERT: C 42 GLU cc_start: 0.7869 (mp0) cc_final: 0.7619 (mp0) REVERT: C 62 GLU cc_start: 0.7160 (tt0) cc_final: 0.6939 (mt-10) REVERT: D 74 ILE cc_start: 0.9025 (mm) cc_final: 0.8770 (tt) REVERT: D 84 TYR cc_start: 0.6411 (m-80) cc_final: 0.6082 (m-10) REVERT: D 86 LYS cc_start: 0.9173 (tptt) cc_final: 0.8898 (tppp) REVERT: D 121 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8849 (tmtt) REVERT: E 73 ARG cc_start: 0.5497 (mtt-85) cc_final: 0.5014 (mtt90) REVERT: E 77 GLN cc_start: 0.8880 (tt0) cc_final: 0.8284 (tp40) REVERT: F 53 GLU cc_start: 0.8392 (pm20) cc_final: 0.7921 (pm20) REVERT: K 1 MET cc_start: 0.3809 (mpp) cc_final: 0.3589 (mpp) REVERT: K 111 ARG cc_start: 0.2083 (tpt170) cc_final: 0.0985 (mmt90) REVERT: K 151 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8117 (mm-30) REVERT: K 814 LEU cc_start: 0.5720 (mt) cc_final: 0.5466 (mt) REVERT: K 821 LEU cc_start: 0.6215 (mm) cc_final: 0.5612 (mm) REVERT: K 844 LYS cc_start: 0.7085 (mmtm) cc_final: 0.6572 (mtmt) REVERT: K 873 MET cc_start: 0.5513 (mtm) cc_final: 0.4118 (mpp) REVERT: K 910 MET cc_start: 0.6277 (ptp) cc_final: 0.5457 (pmm) REVERT: K 959 ILE cc_start: 0.3503 (mt) cc_final: 0.3163 (mt) REVERT: K 977 CYS cc_start: 0.7496 (m) cc_final: 0.7180 (m) REVERT: L 77 LYS cc_start: 0.7008 (mtmt) cc_final: 0.6422 (mttm) REVERT: L 198 ASP cc_start: 0.8385 (m-30) cc_final: 0.8103 (m-30) REVERT: L 214 ARG cc_start: 0.8498 (mtt90) cc_final: 0.7625 (mtp-110) REVERT: L 288 ARG cc_start: 0.7702 (mtt90) cc_final: 0.7155 (mtm110) REVERT: L 376 ASP cc_start: 0.7024 (t70) cc_final: 0.6719 (t70) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.8040 time to fit residues: 404.9735 Evaluate side-chains 301 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 7.9990 chunk 128 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 0.0570 chunk 220 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- 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** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22474 Z= 0.205 Angle : 0.623 7.637 31615 Z= 0.372 Chirality : 0.041 0.161 3569 Planarity : 0.004 0.054 3037 Dihedral : 27.334 177.565 5404 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.50 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.36 (0.19), residues: 1947 helix: 0.26 (0.21), residues: 625 sheet: -0.69 (0.24), residues: 446 loop : -1.86 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 256 HIS 0.012 0.001 HIS K 789 PHE 0.019 0.002 PHE L 110 TYR 0.016 0.002 TYR D 84 ARG 0.007 0.000 ARG C 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.832 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: A 56 GLN cc_start: 0.9247 (mt0) cc_final: 0.8619 (mt0) REVERT: A 57 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7630 (mmtt) REVERT: A 98 GLU cc_start: 0.8816 (pp20) cc_final: 0.8523 (pp20) REVERT: C 37 LYS cc_start: 0.6207 (mttm) cc_final: 0.5782 (tmtt) REVERT: C 39 ASN cc_start: 0.8226 (m-40) cc_final: 0.7974 (m110) REVERT: C 42 GLU cc_start: 0.7932 (mp0) cc_final: 0.7728 (mp0) REVERT: C 62 GLU cc_start: 0.7104 (tt0) cc_final: 0.6899 (mt-10) REVERT: D 36 GLU cc_start: 0.7091 (pp20) cc_final: 0.6276 (pp20) REVERT: D 74 ILE cc_start: 0.9022 (mm) cc_final: 0.8771 (tt) REVERT: D 84 TYR cc_start: 0.6308 (m-80) cc_final: 0.5965 (m-10) REVERT: D 86 LYS cc_start: 0.9168 (tptt) cc_final: 0.8894 (tppp) REVERT: D 121 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8915 (tmtt) REVERT: E 73 ARG cc_start: 0.5459 (mtt-85) cc_final: 0.4968 (mtt90) REVERT: E 77 GLN cc_start: 0.8840 (tt0) cc_final: 0.8245 (tp40) REVERT: F 51 ILE cc_start: 0.8586 (mm) cc_final: 0.8375 (mm) REVERT: F 53 GLU cc_start: 0.8208 (pm20) cc_final: 0.7797 (pm20) REVERT: H 36 GLU cc_start: 0.7378 (pp20) cc_final: 0.7162 (pt0) REVERT: K 1 MET cc_start: 0.3895 (mpp) cc_final: 0.3453 (mpp) REVERT: K 151 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8068 (mm-30) REVERT: K 210 GLU cc_start: 0.5675 (mm-30) cc_final: 0.5365 (mp0) REVERT: K 288 GLU cc_start: 0.4243 (tp30) cc_final: 0.2388 (pt0) REVERT: K 298 LYS cc_start: 0.6846 (tttt) cc_final: 0.6442 (ttpt) REVERT: K 814 LEU cc_start: 0.5733 (mt) cc_final: 0.5459 (mt) REVERT: K 844 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6670 (mtmt) REVERT: K 873 MET cc_start: 0.5101 (mtm) cc_final: 0.4020 (mpp) REVERT: K 899 LEU cc_start: 0.2355 (mt) cc_final: 0.2135 (mt) REVERT: K 910 MET cc_start: 0.6552 (ptp) cc_final: 0.5828 (pmm) REVERT: K 959 ILE cc_start: 0.3406 (mt) cc_final: 0.3050 (mt) REVERT: K 977 CYS cc_start: 0.7314 (m) cc_final: 0.7108 (m) REVERT: K 995 VAL cc_start: 0.8149 (m) cc_final: 0.7894 (p) REVERT: K 1014 MET cc_start: 0.4025 (tpp) cc_final: 0.2852 (mtp) REVERT: L 77 LYS cc_start: 0.6960 (mtmt) cc_final: 0.6374 (mttm) REVERT: L 198 ASP cc_start: 0.8421 (m-30) cc_final: 0.8130 (m-30) REVERT: L 214 ARG cc_start: 0.8475 (mtt90) cc_final: 0.7593 (mtp-110) REVERT: L 270 TRP cc_start: 0.5965 (m100) cc_final: 0.3290 (m100) REVERT: L 288 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7119 (mtm110) REVERT: L 376 ASP cc_start: 0.6802 (t70) cc_final: 0.6475 (t70) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.7689 time to fit residues: 387.6946 Evaluate side-chains 299 residues out of total 1684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 180 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 154 optimal weight: 8.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- 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** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.175675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.138457 restraints weight = 110137.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.146490 restraints weight = 45359.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.151734 restraints weight = 23979.248| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22474 Z= 0.208 Angle : 0.619 7.503 31615 Z= 0.371 Chirality : 0.041 0.161 3569 Planarity : 0.005 0.067 3037 Dihedral : 27.291 177.224 5404 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.30 (0.19), residues: 1947 helix: 0.37 (0.20), residues: 623 sheet: -0.68 (0.24), residues: 459 loop : -1.88 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 207 HIS 0.011 0.001 HIS K 789 PHE 0.021 0.002 PHE B 101 TYR 0.015 0.002 TYR D 84 ARG 0.012 0.000 ARG K 928 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10380.54 seconds wall clock time: 183 minutes 37.13 seconds (11017.13 seconds total)