Starting phenix.real_space_refine on Sun Mar 17 05:18:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djb_27459/03_2024/8djb_27459.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians K 1 8.98 5 S 68 5.16 5 C 10576 2.51 5 N 2896 2.21 5 O 3240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 16781 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "G" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.60, per 1000 atoms: 0.51 Number of scatterers: 16781 At special positions: 0 Unit cell: (144.039, 144.039, 119.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 S 68 16.00 O 3240 8.00 N 2896 7.00 C 10576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 3.1 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 51.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 107 removed outlier: 4.174A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 145 through 156 removed outlier: 3.689A pdb=" N ARG D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 145 through 156 removed outlier: 3.689A pdb=" N ARG F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 247 through 257 Processing helix chain 'F' and resid 279 through 284 Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 130 Processing helix chain 'H' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG H 149 " --> pdb=" O ASP H 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'H' and resid 247 through 257 Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 323 through 334 Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 107 removed outlier: 4.175A pdb=" N MET G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 130 Processing helix chain 'G' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.668A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 230 through 242 Processing helix chain 'G' and resid 247 through 257 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.730A pdb=" N GLY C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 107 removed outlier: 4.174A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.667A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'E' and resid 21 through 39 removed outlier: 3.731A pdb=" N GLY E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 39 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 58 removed outlier: 3.584A pdb=" N TYR E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 107 removed outlier: 4.175A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 Processing helix chain 'E' and resid 145 through 156 removed outlier: 3.690A pdb=" N ARG E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.667A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE B 317 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 296 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE D 317 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL D 296 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE F 317 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL F 296 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AB1, first strand: chain 'H' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE H 317 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL H 296 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU H 319 " --> pdb=" O ILE H 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.363A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AB5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AB7, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.364A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2948 1.31 - 1.43: 4018 1.43 - 1.56: 9942 1.56 - 1.68: 0 1.68 - 1.81: 112 Bond restraints: 17020 Sorted by residual: bond pdb=" C ILE E 229 " pdb=" O ILE E 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.83e+01 bond pdb=" C ILE H 229 " pdb=" O ILE H 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.79e+01 bond pdb=" C ILE B 229 " pdb=" O ILE B 229 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.02e-02 9.61e+03 2.79e+01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.02e-02 9.61e+03 2.75e+01 bond pdb=" C ILE G 229 " pdb=" O ILE G 229 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.02e-02 9.61e+03 2.74e+01 ... (remaining 17015 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.40: 516 107.40 - 114.05: 9944 114.05 - 120.69: 6768 120.69 - 127.34: 5696 127.34 - 133.98: 100 Bond angle restraints: 23024 Sorted by residual: angle pdb=" N TYR G 74 " pdb=" CA TYR G 74 " pdb=" C TYR G 74 " ideal model delta sigma weight residual 111.14 105.33 5.81 1.08e+00 8.57e-01 2.89e+01 angle pdb=" N TYR C 74 " pdb=" CA TYR C 74 " pdb=" C TYR C 74 " ideal model delta sigma weight residual 111.14 105.34 5.80 1.08e+00 8.57e-01 2.88e+01 angle pdb=" N TYR A 74 " pdb=" CA TYR A 74 " pdb=" C TYR A 74 " ideal model delta sigma weight residual 111.14 105.34 5.80 1.08e+00 8.57e-01 2.88e+01 angle pdb=" N TYR E 74 " pdb=" CA TYR E 74 " pdb=" C TYR E 74 " ideal model delta sigma weight residual 111.14 105.35 5.79 1.08e+00 8.57e-01 2.87e+01 angle pdb=" C ARG E 313 " pdb=" CA ARG E 313 " pdb=" CB ARG E 313 " ideal model delta sigma weight residual 114.41 106.34 8.07 2.30e+00 1.89e-01 1.23e+01 ... (remaining 23019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 9652 17.79 - 35.58: 484 35.58 - 53.36: 136 53.36 - 71.15: 68 71.15 - 88.94: 4 Dihedral angle restraints: 10344 sinusoidal: 4192 harmonic: 6152 Sorted by residual: dihedral pdb=" CG ARG B 116 " pdb=" CD ARG B 116 " pdb=" NE ARG B 116 " pdb=" CZ ARG B 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.08 -61.92 2 1.50e+01 4.44e-03 1.66e+01 dihedral pdb=" CG ARG C 116 " pdb=" CD ARG C 116 " pdb=" NE ARG C 116 " pdb=" CZ ARG C 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.12 -61.88 2 1.50e+01 4.44e-03 1.66e+01 dihedral pdb=" CG ARG H 116 " pdb=" CD ARG H 116 " pdb=" NE ARG H 116 " pdb=" CZ ARG H 116 " ideal model delta sinusoidal sigma weight residual -90.00 -28.12 -61.88 2 1.50e+01 4.44e-03 1.66e+01 ... (remaining 10341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2374 0.077 - 0.155: 276 0.155 - 0.232: 26 0.232 - 0.310: 8 0.310 - 0.387: 8 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA GLU H 144 " pdb=" N GLU H 144 " pdb=" C GLU H 144 " pdb=" CB GLU H 144 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA GLU D 144 " pdb=" N GLU D 144 " pdb=" C GLU D 144 " pdb=" CB GLU D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLU A 144 " pdb=" N GLU A 144 " pdb=" C GLU A 144 " pdb=" CB GLU A 144 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2689 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 240 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C SER B 240 " -0.037 2.00e-02 2.50e+03 pdb=" O SER B 240 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 241 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 240 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C SER F 240 " 0.037 2.00e-02 2.50e+03 pdb=" O SER F 240 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG F 241 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 240 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C SER H 240 " -0.037 2.00e-02 2.50e+03 pdb=" O SER H 240 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG H 241 " 0.012 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.55: 68 2.55 - 3.20: 15006 3.20 - 3.85: 30223 3.85 - 4.49: 42350 4.49 - 5.14: 71893 Nonbonded interactions: 159540 Sorted by model distance: nonbonded pdb=" CB ARG C 135 " pdb=" OE2 GLU C 138 " model vdw 1.908 3.440 nonbonded pdb=" CB ARG G 135 " pdb=" OE2 GLU G 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG E 135 " pdb=" OE2 GLU E 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG F 135 " pdb=" OE2 GLU F 138 " model vdw 1.909 3.440 nonbonded pdb=" CB ARG B 135 " pdb=" OE2 GLU B 138 " model vdw 1.909 3.440 ... (remaining 159535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 20 through 336) selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.010 Extract box with map and model: 6.560 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 45.350 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.054 17020 Z= 0.355 Angle : 0.724 8.161 23024 Z= 0.471 Chirality : 0.055 0.387 2692 Planarity : 0.004 0.021 2988 Dihedral : 12.904 88.941 6392 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 6.96 % Allowed : 6.52 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2140 helix: 0.21 (0.16), residues: 1036 sheet: 0.55 (0.33), residues: 304 loop : -1.69 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 52 HIS 0.002 0.001 HIS C 193 PHE 0.006 0.001 PHE C 87 TYR 0.025 0.002 TYR E 51 ARG 0.005 0.000 ARG F 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 466 time to evaluate : 1.880 Fit side-chains REVERT: A 25 LEU cc_start: 0.9053 (mp) cc_final: 0.8780 (tt) REVERT: A 98 LEU cc_start: 0.8720 (tp) cc_final: 0.8506 (tp) REVERT: B 229 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7761 (mm) REVERT: B 310 TYR cc_start: 0.8797 (t80) cc_final: 0.8549 (t80) REVERT: D 229 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7690 (mm) REVERT: D 310 TYR cc_start: 0.8782 (t80) cc_final: 0.8528 (t80) REVERT: F 229 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7725 (mm) REVERT: F 310 TYR cc_start: 0.8778 (t80) cc_final: 0.8524 (t80) REVERT: H 170 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8352 (mp) REVERT: H 229 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7795 (mm) REVERT: H 310 TYR cc_start: 0.8828 (t80) cc_final: 0.8565 (t80) REVERT: G 38 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: G 76 THR cc_start: 0.8910 (m) cc_final: 0.8521 (m) REVERT: G 80 ILE cc_start: 0.9387 (mt) cc_final: 0.9171 (mt) REVERT: G 102 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 25 LEU cc_start: 0.8927 (mp) cc_final: 0.8697 (tt) REVERT: C 80 ILE cc_start: 0.9395 (mt) cc_final: 0.9173 (mt) REVERT: E 25 LEU cc_start: 0.8999 (mp) cc_final: 0.8743 (tt) REVERT: E 38 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6609 (m-10) outliers start: 128 outliers final: 26 residues processed: 570 average time/residue: 0.3765 time to fit residues: 291.8699 Evaluate side-chains 289 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17020 Z= 0.228 Angle : 0.617 12.868 23024 Z= 0.305 Chirality : 0.047 0.154 2692 Planarity : 0.004 0.028 2988 Dihedral : 5.566 59.836 2444 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.45 % Allowed : 14.18 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.18), residues: 2140 helix: 0.97 (0.16), residues: 1016 sheet: 0.43 (0.31), residues: 304 loop : -1.38 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 52 HIS 0.004 0.001 HIS A 39 PHE 0.024 0.002 PHE C 40 TYR 0.038 0.002 TYR C 74 ARG 0.006 0.001 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 265 time to evaluate : 2.017 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8185 (m-10) cc_final: 0.7772 (m-80) REVERT: B 275 LEU cc_start: 0.8393 (mp) cc_final: 0.8157 (mp) REVERT: F 275 LEU cc_start: 0.8423 (mp) cc_final: 0.8175 (mp) REVERT: G 74 TYR cc_start: 0.8246 (m-80) cc_final: 0.7901 (m-80) REVERT: G 104 MET cc_start: 0.7995 (tpp) cc_final: 0.7789 (ttp) REVERT: G 107 MET cc_start: 0.8254 (ptp) cc_final: 0.8018 (ptt) REVERT: C 74 TYR cc_start: 0.8248 (m-80) cc_final: 0.7924 (m-80) REVERT: C 104 MET cc_start: 0.7972 (tpp) cc_final: 0.7704 (ttp) REVERT: E 74 TYR cc_start: 0.8145 (m-80) cc_final: 0.7858 (m-80) REVERT: E 76 THR cc_start: 0.8841 (m) cc_final: 0.8625 (m) REVERT: E 82 LEU cc_start: 0.9285 (mm) cc_final: 0.9072 (mm) outliers start: 45 outliers final: 25 residues processed: 298 average time/residue: 0.3321 time to fit residues: 143.0852 Evaluate side-chains 246 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN C 103 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17020 Z= 0.352 Angle : 0.631 14.440 23024 Z= 0.319 Chirality : 0.048 0.244 2692 Planarity : 0.004 0.047 2988 Dihedral : 5.009 56.578 2402 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.55 % Allowed : 15.33 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2140 helix: 1.11 (0.16), residues: 1012 sheet: 0.29 (0.29), residues: 304 loop : -1.19 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 52 HIS 0.003 0.001 HIS A 39 PHE 0.023 0.002 PHE A 75 TYR 0.022 0.002 TYR E 74 ARG 0.008 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.160 Fit side-chains REVERT: A 38 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: A 74 TYR cc_start: 0.8222 (m-10) cc_final: 0.7746 (m-80) REVERT: G 74 TYR cc_start: 0.8226 (m-80) cc_final: 0.7972 (m-80) REVERT: G 90 LEU cc_start: 0.8983 (tt) cc_final: 0.8745 (tp) REVERT: C 74 TYR cc_start: 0.8239 (m-80) cc_final: 0.7999 (m-80) REVERT: C 90 LEU cc_start: 0.8892 (tt) cc_final: 0.8672 (tp) REVERT: E 90 LEU cc_start: 0.9003 (tt) cc_final: 0.8727 (tp) outliers start: 47 outliers final: 22 residues processed: 275 average time/residue: 0.3362 time to fit residues: 133.6193 Evaluate side-chains 237 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17020 Z= 0.271 Angle : 0.562 12.976 23024 Z= 0.275 Chirality : 0.046 0.150 2692 Planarity : 0.003 0.023 2988 Dihedral : 4.245 58.659 2386 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 17.01 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2140 helix: 1.27 (0.16), residues: 1012 sheet: 0.39 (0.29), residues: 304 loop : -1.13 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 46 HIS 0.009 0.001 HIS G 39 PHE 0.024 0.001 PHE A 40 TYR 0.039 0.002 TYR E 74 ARG 0.004 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.001 Fit side-chains REVERT: A 38 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: A 74 TYR cc_start: 0.8313 (m-10) cc_final: 0.7765 (m-80) REVERT: A 105 LYS cc_start: 0.8794 (tttt) cc_final: 0.8566 (tttm) REVERT: H 308 ARG cc_start: 0.8180 (ptp-110) cc_final: 0.7921 (ptm160) REVERT: G 74 TYR cc_start: 0.8314 (m-80) cc_final: 0.8037 (m-80) REVERT: G 105 LYS cc_start: 0.8826 (tttt) cc_final: 0.8574 (tttm) REVERT: C 74 TYR cc_start: 0.8280 (m-80) cc_final: 0.8051 (m-80) REVERT: C 105 LYS cc_start: 0.8837 (tttt) cc_final: 0.8602 (tttm) REVERT: E 74 TYR cc_start: 0.7961 (m-80) cc_final: 0.7714 (m-80) REVERT: E 105 LYS cc_start: 0.8760 (tttt) cc_final: 0.8523 (tttm) outliers start: 40 outliers final: 24 residues processed: 257 average time/residue: 0.3149 time to fit residues: 117.7001 Evaluate side-chains 231 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17020 Z= 0.324 Angle : 0.580 13.301 23024 Z= 0.283 Chirality : 0.047 0.224 2692 Planarity : 0.004 0.040 2988 Dihedral : 4.256 56.633 2386 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.07 % Allowed : 17.28 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2140 helix: 1.17 (0.16), residues: 1036 sheet: 0.61 (0.29), residues: 304 loop : -1.11 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 52 HIS 0.014 0.001 HIS A 39 PHE 0.009 0.001 PHE E 54 TYR 0.039 0.002 TYR E 74 ARG 0.005 0.001 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 227 time to evaluate : 2.082 Fit side-chains REVERT: A 38 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: A 74 TYR cc_start: 0.8290 (m-10) cc_final: 0.7941 (m-80) REVERT: G 74 TYR cc_start: 0.8339 (m-80) cc_final: 0.8112 (m-80) REVERT: G 105 LYS cc_start: 0.8888 (tttt) cc_final: 0.8683 (tttm) REVERT: C 40 PHE cc_start: 0.8123 (t80) cc_final: 0.7849 (t80) REVERT: C 105 LYS cc_start: 0.8844 (tttt) cc_final: 0.8618 (tttm) REVERT: E 74 TYR cc_start: 0.7995 (m-80) cc_final: 0.7709 (m-80) outliers start: 38 outliers final: 30 residues processed: 254 average time/residue: 0.2853 time to fit residues: 108.1144 Evaluate side-chains 249 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 317 ILE Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17020 Z= 0.175 Angle : 0.543 13.544 23024 Z= 0.259 Chirality : 0.045 0.174 2692 Planarity : 0.003 0.024 2988 Dihedral : 4.113 57.306 2386 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.01 % Allowed : 17.07 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2140 helix: 1.31 (0.16), residues: 1036 sheet: 0.67 (0.30), residues: 304 loop : -1.06 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 52 HIS 0.003 0.001 HIS A 39 PHE 0.017 0.001 PHE A 40 TYR 0.033 0.001 TYR E 74 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 2.014 Fit side-chains REVERT: A 38 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 74 TYR cc_start: 0.8300 (m-10) cc_final: 0.7890 (m-80) REVERT: G 74 TYR cc_start: 0.8363 (m-80) cc_final: 0.8147 (m-80) REVERT: C 40 PHE cc_start: 0.8037 (t80) cc_final: 0.7728 (t80) REVERT: C 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8603 (tttp) REVERT: E 74 TYR cc_start: 0.8082 (m-80) cc_final: 0.7686 (m-80) outliers start: 37 outliers final: 27 residues processed: 253 average time/residue: 0.2955 time to fit residues: 110.6616 Evaluate side-chains 245 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17020 Z= 0.235 Angle : 0.551 13.716 23024 Z= 0.263 Chirality : 0.045 0.186 2692 Planarity : 0.003 0.028 2988 Dihedral : 4.097 57.496 2386 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.12 % Allowed : 17.23 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2140 helix: 1.36 (0.16), residues: 1036 sheet: 0.71 (0.29), residues: 304 loop : -1.04 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 52 HIS 0.004 0.001 HIS A 39 PHE 0.011 0.001 PHE C 75 TYR 0.043 0.002 TYR C 74 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 1.996 Fit side-chains REVERT: A 38 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: A 40 PHE cc_start: 0.7129 (t80) cc_final: 0.6853 (t80) REVERT: A 74 TYR cc_start: 0.8244 (m-10) cc_final: 0.7829 (m-80) REVERT: G 74 TYR cc_start: 0.8455 (m-80) cc_final: 0.8198 (m-80) REVERT: C 40 PHE cc_start: 0.8097 (t80) cc_final: 0.7782 (t80) REVERT: C 105 LYS cc_start: 0.8821 (tttt) cc_final: 0.8615 (tttp) REVERT: E 74 TYR cc_start: 0.8041 (m-80) cc_final: 0.7602 (m-80) outliers start: 39 outliers final: 32 residues processed: 254 average time/residue: 0.2986 time to fit residues: 112.0723 Evaluate side-chains 251 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN H 332 ASN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17020 Z= 0.166 Angle : 0.543 14.919 23024 Z= 0.256 Chirality : 0.045 0.180 2692 Planarity : 0.003 0.027 2988 Dihedral : 4.020 59.891 2386 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.17 % Allowed : 17.28 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 2140 helix: 1.52 (0.16), residues: 1036 sheet: 0.72 (0.29), residues: 304 loop : -1.02 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.002 0.000 HIS C 39 PHE 0.006 0.001 PHE E 40 TYR 0.029 0.001 TYR E 74 ARG 0.004 0.000 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 2.098 Fit side-chains REVERT: A 38 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: A 40 PHE cc_start: 0.7069 (t80) cc_final: 0.6836 (t80) REVERT: A 103 GLN cc_start: 0.8484 (tp40) cc_final: 0.8178 (tp40) REVERT: G 74 TYR cc_start: 0.8480 (m-80) cc_final: 0.8161 (m-80) REVERT: C 40 PHE cc_start: 0.8081 (t80) cc_final: 0.7751 (t80) REVERT: E 57 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (tp) outliers start: 40 outliers final: 26 residues processed: 254 average time/residue: 0.2961 time to fit residues: 111.5583 Evaluate side-chains 246 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN G 103 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17020 Z= 0.232 Angle : 0.565 13.925 23024 Z= 0.265 Chirality : 0.045 0.192 2692 Planarity : 0.003 0.028 2988 Dihedral : 4.065 58.526 2386 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.58 % Allowed : 18.04 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2140 helix: 1.44 (0.16), residues: 1036 sheet: 0.76 (0.29), residues: 304 loop : -1.03 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 52 HIS 0.003 0.001 HIS C 39 PHE 0.007 0.001 PHE A 54 TYR 0.023 0.001 TYR C 51 ARG 0.004 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 219 time to evaluate : 1.983 Fit side-chains REVERT: A 38 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: A 103 GLN cc_start: 0.8499 (tp40) cc_final: 0.8196 (tp40) REVERT: G 74 TYR cc_start: 0.8449 (m-80) cc_final: 0.8094 (m-80) REVERT: C 40 PHE cc_start: 0.8098 (t80) cc_final: 0.7799 (t80) REVERT: C 74 TYR cc_start: 0.8288 (m-80) cc_final: 0.7583 (m-80) REVERT: C 105 LYS cc_start: 0.8808 (tttp) cc_final: 0.8505 (ttmt) REVERT: E 74 TYR cc_start: 0.8241 (m-80) cc_final: 0.7573 (m-80) REVERT: E 103 GLN cc_start: 0.8517 (tp40) cc_final: 0.8234 (tp40) outliers start: 29 outliers final: 25 residues processed: 243 average time/residue: 0.3133 time to fit residues: 113.5380 Evaluate side-chains 243 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17020 Z= 0.179 Angle : 0.558 14.164 23024 Z= 0.259 Chirality : 0.045 0.194 2692 Planarity : 0.003 0.030 2988 Dihedral : 4.010 58.708 2386 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.47 % Allowed : 18.32 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2140 helix: 1.53 (0.16), residues: 1036 sheet: 0.75 (0.29), residues: 304 loop : -1.00 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 52 HIS 0.004 0.001 HIS A 39 PHE 0.007 0.001 PHE E 54 TYR 0.023 0.001 TYR C 51 ARG 0.003 0.000 ARG F 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.884 Fit side-chains REVERT: A 38 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: A 103 GLN cc_start: 0.8483 (tp40) cc_final: 0.8189 (tp40) REVERT: B 308 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: G 74 TYR cc_start: 0.8468 (m-80) cc_final: 0.8071 (m-80) REVERT: C 40 PHE cc_start: 0.8133 (t80) cc_final: 0.7800 (t80) REVERT: C 74 TYR cc_start: 0.8250 (m-80) cc_final: 0.7840 (m-80) REVERT: C 105 LYS cc_start: 0.8767 (tttp) cc_final: 0.8493 (ttmt) REVERT: E 57 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8336 (tp) REVERT: E 74 TYR cc_start: 0.8214 (m-80) cc_final: 0.7516 (m-80) REVERT: E 103 GLN cc_start: 0.8502 (tp40) cc_final: 0.8239 (tp40) outliers start: 27 outliers final: 23 residues processed: 246 average time/residue: 0.3045 time to fit residues: 110.3585 Evaluate side-chains 241 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain G residue 38 PHE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 332 ASN G 103 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076323 restraints weight = 27399.423| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.17 r_work: 0.2798 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17020 Z= 0.163 Angle : 0.553 13.969 23024 Z= 0.255 Chirality : 0.045 0.187 2692 Planarity : 0.003 0.033 2988 Dihedral : 3.969 58.859 2386 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.41 % Allowed : 18.42 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2140 helix: 1.60 (0.16), residues: 1036 sheet: 0.77 (0.29), residues: 304 loop : -0.97 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 52 HIS 0.002 0.000 HIS G 39 PHE 0.007 0.001 PHE E 54 TYR 0.023 0.001 TYR C 51 ARG 0.003 0.000 ARG G 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.46 seconds wall clock time: 70 minutes 55.20 seconds (4255.20 seconds total)