Starting phenix.real_space_refine on Fri Mar 15 01:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/03_2024/7k2t_22644_updated.pdb" } resolution = 3.6 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= 0.006 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 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6842 2.51 5 N 1607 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 119": "OD1" <-> "OD2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 249": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10275 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3005 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain breaks: 2 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2082 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2993 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 2 Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.80, per 1000 atoms: 0.56 Number of scatterers: 10275 At special positions: 0 Unit cell: (101.363, 79.0034, 138.629, 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 28 16.00 P 6 15.00 Mg 2 11.99 O 1790 8.00 N 1607 7.00 C 6842 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 12 sheets defined 45.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.706A pdb=" N GLU A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 22 through 46 removed outlier: 4.065A pdb=" N TRP B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 4.514A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 85 removed outlier: 3.792A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.827A pdb=" N THR B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 127 Proline residue: B 103 - end of helix removed outlier: 3.564A pdb=" N ILE B 107 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B 109 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 120 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 162 removed outlier: 5.180A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Proline residue: B 141 - end of helix removed outlier: 3.572A pdb=" N ILE B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 155 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 162 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.767A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.885A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 224 through 255 Proline residue: B 235 - end of helix removed outlier: 3.681A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.538A pdb=" N LYS C 22 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 23 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.673A pdb=" N ASP C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 27 through 43 Proline residue: D 32 - end of helix removed outlier: 3.553A pdb=" N PHE D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 99 through 128 Proline residue: D 103 - end of helix removed outlier: 3.869A pdb=" N ILE D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 116 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 117 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 127 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 134 through 164 removed outlier: 5.035A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Proline residue: D 141 - end of helix removed outlier: 4.653A pdb=" N TYR D 150 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D 151 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE D 154 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 155 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY D 159 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 162 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 4.759A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.513A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 200' Processing helix chain 'D' and resid 204 through 216 removed outlier: 4.445A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 254 removed outlier: 3.626A pdb=" N ALA D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.652A pdb=" N SER D 241 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 5.640A pdb=" N ILE A 40 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 218 through 223 removed outlier: 6.458A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 197 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 278 through 280 removed outlier: 3.948A pdb=" N ASP A 278 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 326 through 331 removed outlier: 3.606A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 367 through 371 removed outlier: 3.913A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 350 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 296 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 8 through 11 removed outlier: 7.079A pdb=" N TYR A 11 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TRP A 35 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.740A pdb=" N ILE C 2 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 40 " --> pdb=" O ASP C 6 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 50 through 54 removed outlier: 7.066A pdb=" N ARG C 210 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL C 53 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 212 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS C 215 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 219 " --> pdb=" O HIS C 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.630A pdb=" N CYS C 162 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU C 87 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 164 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER C 193 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ILE C 165 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 195 " --> pdb=" O ILE C 165 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 326 through 336 removed outlier: 3.980A pdb=" N ASP C 278 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 368 through 371 removed outlier: 3.527A pdb=" N PHE C 310 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.888A pdb=" N TYR C 11 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TRP C 35 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 13 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU C 33 " --> pdb=" O TYR C 13 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1044 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: 2.72 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3058 1.34 - 1.46: 2468 1.46 - 1.58: 4957 1.58 - 1.69: 10 1.69 - 1.81: 46 Bond restraints: 10539 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C5 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 10534 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.87: 275 106.87 - 114.18: 6133 114.18 - 121.48: 5652 121.48 - 128.79: 2132 128.79 - 136.09: 73 Bond angle restraints: 14265 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.18 21.69 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 118.26 18.57 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 118.49 18.34 1.00e+00 1.00e+00 3.36e+02 angle pdb=" C5 ATP A 501 " pdb=" C4 ATP A 501 " pdb=" N3 ATP A 501 " ideal model delta sigma weight residual 126.80 118.57 8.23 1.00e+00 1.00e+00 6.77e+01 ... (remaining 14260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5543 17.55 - 35.09: 547 35.09 - 52.64: 84 52.64 - 70.19: 22 70.19 - 87.73: 11 Dihedral angle restraints: 6207 sinusoidal: 2571 harmonic: 3636 Sorted by residual: dihedral pdb=" CA LEU C 98 " pdb=" C LEU C 98 " pdb=" N SER C 99 " pdb=" CA SER C 99 " ideal model delta harmonic sigma weight residual 180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR B 18 " pdb=" C TYR B 18 " pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LYS D 50 " pdb=" C LYS D 50 " pdb=" N LEU D 51 " pdb=" CA LEU D 51 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1124 0.042 - 0.084: 363 0.084 - 0.126: 106 0.126 - 0.168: 11 0.168 - 0.210: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CB ILE C 219 " pdb=" CA ILE C 219 " pdb=" CG1 ILE C 219 " pdb=" CG2 ILE C 219 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 212 " pdb=" N ILE C 212 " pdb=" C ILE C 212 " pdb=" CB ILE C 212 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 363 " pdb=" N ILE A 363 " pdb=" C ILE A 363 " pdb=" CB ILE A 363 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1602 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 132 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.71e+00 pdb=" C ASP C 132 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 132 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP C 133 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 339 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 340 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 146 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C LEU D 146 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU D 146 " -0.008 2.00e-02 2.50e+03 pdb=" N MET D 147 " -0.007 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 80 2.54 - 3.13: 8263 3.13 - 3.72: 15248 3.72 - 4.31: 21972 4.31 - 4.90: 37132 Nonbonded interactions: 82695 Sorted by model distance: nonbonded pdb=" O1G ATP A 501 " pdb="MG MG A 502 " model vdw 1.955 2.170 nonbonded pdb=" O1G ATP C 501 " pdb="MG MG C 502 " model vdw 2.042 2.170 nonbonded pdb=" O1B ATP A 501 " pdb="MG MG A 502 " model vdw 2.079 2.170 nonbonded pdb=" O1B ATP C 501 " pdb="MG MG C 502 " model vdw 2.134 2.170 nonbonded pdb=" OG SER A 61 " pdb="MG MG A 502 " model vdw 2.180 2.170 ... (remaining 82690 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 1 through 241 or resid 255 through 395 or resid 501 throug \ h 502)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 47 or resid 55 through 256)) } 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=0.15 max=1.00 mean=0.98 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: 0.740 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: 0.000 Extract box with map and model: 4.230 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.079 10539 Z= 0.337 Angle : 0.775 21.694 14265 Z= 0.529 Chirality : 0.044 0.210 1605 Planarity : 0.003 0.032 1735 Dihedral : 14.489 87.734 3875 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -3.30 (0.21), residues: 1231 helix: -1.83 (0.19), residues: 604 sheet: -1.78 (0.33), residues: 185 loop : -2.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 71 HIS 0.012 0.001 HIS D 213 PHE 0.017 0.002 PHE D 179 TYR 0.013 0.001 TYR D 63 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7241 (tt0) cc_final: 0.6880 (tp30) REVERT: A 365 ASN cc_start: 0.6626 (p0) cc_final: 0.6421 (p0) REVERT: C 121 LYS cc_start: 0.8879 (mttt) cc_final: 0.8568 (mtpp) REVERT: C 123 GLU cc_start: 0.6424 (mp0) cc_final: 0.6019 (mp0) REVERT: C 146 MET cc_start: 0.8748 (mtp) cc_final: 0.8130 (mtm) REVERT: C 263 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.6332 (mtp85) REVERT: C 350 HIS cc_start: 0.7044 (p90) cc_final: 0.6842 (p-80) REVERT: C 368 ASN cc_start: 0.7508 (t0) cc_final: 0.6704 (m-40) REVERT: C 388 GLU cc_start: 0.8141 (tt0) cc_final: 0.7646 (tt0) REVERT: D 8 GLU cc_start: 0.8220 (tp30) cc_final: 0.7521 (tp30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2768 time to fit residues: 84.8755 Evaluate side-chains 155 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS C 189 GLN C 272 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10539 Z= 0.389 Angle : 0.664 10.130 14265 Z= 0.338 Chirality : 0.046 0.155 1605 Planarity : 0.004 0.032 1735 Dihedral : 9.074 84.554 1408 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.23 % Allowed : 11.78 % Favored : 85.99 % 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: -2.36 (0.22), residues: 1231 helix: -1.03 (0.20), residues: 607 sheet: -1.48 (0.34), residues: 185 loop : -2.18 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 27 HIS 0.011 0.001 HIS D 213 PHE 0.031 0.002 PHE B 131 TYR 0.017 0.002 TYR B 150 ARG 0.003 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7213 (tt0) cc_final: 0.6889 (tp30) REVERT: A 365 ASN cc_start: 0.7539 (p0) cc_final: 0.7259 (p0) REVERT: B 72 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: C 146 MET cc_start: 0.8815 (mtp) cc_final: 0.8204 (mtm) REVERT: C 340 PRO cc_start: 0.8856 (Cg_exo) cc_final: 0.8479 (Cg_endo) REVERT: C 368 ASN cc_start: 0.7577 (t0) cc_final: 0.7058 (m-40) REVERT: D 8 GLU cc_start: 0.8145 (tp30) cc_final: 0.7585 (tp30) REVERT: D 98 ARG cc_start: 0.8403 (tpp80) cc_final: 0.7987 (tpp80) REVERT: D 218 ASN cc_start: 0.8464 (t0) cc_final: 0.8248 (t0) outliers start: 25 outliers final: 17 residues processed: 175 average time/residue: 0.2422 time to fit residues: 58.7126 Evaluate side-chains 165 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 372 ASN Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10539 Z= 0.245 Angle : 0.586 9.517 14265 Z= 0.296 Chirality : 0.043 0.150 1605 Planarity : 0.004 0.028 1735 Dihedral : 8.537 80.058 1408 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.50 % Allowed : 13.56 % Favored : 83.94 % 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: -1.84 (0.23), residues: 1231 helix: -0.65 (0.21), residues: 607 sheet: -1.02 (0.35), residues: 185 loop : -1.95 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 71 HIS 0.008 0.001 HIS D 213 PHE 0.017 0.001 PHE B 131 TYR 0.015 0.001 TYR B 150 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7214 (tt0) cc_final: 0.6905 (tp30) REVERT: A 365 ASN cc_start: 0.7625 (p0) cc_final: 0.7419 (p0) REVERT: B 12 GLN cc_start: 0.8735 (tt0) cc_final: 0.8110 (mt0) REVERT: B 72 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: C 146 MET cc_start: 0.8795 (mtp) cc_final: 0.8463 (mtt) REVERT: C 340 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8443 (Cg_endo) REVERT: D 8 GLU cc_start: 0.8204 (tp30) cc_final: 0.7697 (tp30) REVERT: D 98 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7967 (tpp80) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.2259 time to fit residues: 54.3271 Evaluate side-chains 164 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10539 Z= 0.405 Angle : 0.661 10.642 14265 Z= 0.334 Chirality : 0.045 0.155 1605 Planarity : 0.004 0.029 1735 Dihedral : 8.294 70.631 1408 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.39 % Allowed : 15.88 % Favored : 80.73 % 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: -1.67 (0.23), residues: 1231 helix: -0.60 (0.21), residues: 609 sheet: -0.82 (0.35), residues: 198 loop : -1.81 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 27 HIS 0.009 0.001 HIS D 213 PHE 0.020 0.002 PHE C 163 TYR 0.016 0.002 TYR C 142 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7240 (tt0) cc_final: 0.6964 (tt0) REVERT: B 12 GLN cc_start: 0.8751 (tt0) cc_final: 0.8255 (mt0) REVERT: B 72 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8690 (m-10) REVERT: B 225 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6711 (t80) REVERT: C 123 GLU cc_start: 0.6419 (mp0) cc_final: 0.6019 (mp0) REVERT: C 132 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7871 (p0) REVERT: C 146 MET cc_start: 0.8837 (mtp) cc_final: 0.8220 (mtm) REVERT: C 212 ILE cc_start: 0.8956 (mm) cc_final: 0.8538 (tt) REVERT: C 340 PRO cc_start: 0.8853 (Cg_exo) cc_final: 0.8488 (Cg_endo) REVERT: D 8 GLU cc_start: 0.8225 (tp30) cc_final: 0.7700 (tp30) REVERT: D 98 ARG cc_start: 0.8356 (tpp80) cc_final: 0.8103 (tpp80) outliers start: 38 outliers final: 28 residues processed: 166 average time/residue: 0.2175 time to fit residues: 51.5230 Evaluate side-chains 162 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0040 chunk 1 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 241 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10539 Z= 0.165 Angle : 0.554 9.788 14265 Z= 0.279 Chirality : 0.042 0.149 1605 Planarity : 0.003 0.026 1735 Dihedral : 7.681 71.187 1408 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.66 % Allowed : 16.32 % Favored : 80.02 % 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: -1.25 (0.24), residues: 1231 helix: -0.25 (0.21), residues: 605 sheet: -0.60 (0.35), residues: 200 loop : -1.62 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 71 HIS 0.019 0.001 HIS D 45 PHE 0.011 0.001 PHE D 182 TYR 0.023 0.001 TYR C 328 ARG 0.003 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7428 (t0) REVERT: A 222 GLU cc_start: 0.7197 (tt0) cc_final: 0.6927 (tt0) REVERT: A 241 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.5930 (m110) REVERT: B 72 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8802 (m-10) REVERT: B 225 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6579 (t80) REVERT: C 132 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7642 (p0) REVERT: C 146 MET cc_start: 0.8739 (mtp) cc_final: 0.8181 (mtm) REVERT: C 263 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6376 (mtp85) REVERT: C 379 PHE cc_start: 0.8637 (p90) cc_final: 0.8285 (p90) REVERT: D 8 GLU cc_start: 0.8189 (tp30) cc_final: 0.7711 (tp30) REVERT: D 72 PHE cc_start: 0.8261 (m-10) cc_final: 0.7980 (m-80) REVERT: D 98 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7989 (tpp80) outliers start: 41 outliers final: 23 residues processed: 188 average time/residue: 0.2198 time to fit residues: 58.2303 Evaluate side-chains 170 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10539 Z= 0.243 Angle : 0.587 10.507 14265 Z= 0.295 Chirality : 0.043 0.156 1605 Planarity : 0.004 0.028 1735 Dihedral : 7.440 68.266 1408 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.93 % Allowed : 16.86 % Favored : 79.21 % 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: -1.11 (0.24), residues: 1231 helix: -0.16 (0.22), residues: 600 sheet: -0.61 (0.36), residues: 205 loop : -1.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 71 HIS 0.006 0.001 HIS D 213 PHE 0.013 0.001 PHE C 163 TYR 0.014 0.001 TYR C 328 ARG 0.004 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7504 (t0) REVERT: A 222 GLU cc_start: 0.7219 (tt0) cc_final: 0.6958 (tt0) REVERT: B 72 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8839 (m-10) REVERT: B 170 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 225 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6666 (t80) REVERT: C 123 GLU cc_start: 0.6112 (mp0) cc_final: 0.5758 (mp0) REVERT: C 132 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7776 (p0) REVERT: C 146 MET cc_start: 0.8773 (mtp) cc_final: 0.8427 (mtt) REVERT: C 263 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6390 (mtp85) REVERT: C 379 PHE cc_start: 0.8599 (p90) cc_final: 0.8366 (p90) REVERT: D 8 GLU cc_start: 0.8217 (tp30) cc_final: 0.7708 (tp30) outliers start: 44 outliers final: 28 residues processed: 175 average time/residue: 0.2152 time to fit residues: 53.2806 Evaluate side-chains 174 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 241 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10539 Z= 0.180 Angle : 0.556 9.440 14265 Z= 0.278 Chirality : 0.042 0.162 1605 Planarity : 0.003 0.024 1735 Dihedral : 7.156 64.838 1408 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.94 % Allowed : 17.75 % Favored : 79.30 % 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: -0.98 (0.24), residues: 1231 helix: -0.09 (0.22), residues: 606 sheet: -0.42 (0.36), residues: 206 loop : -1.42 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 71 HIS 0.006 0.001 HIS D 213 PHE 0.011 0.001 PHE C 163 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 6 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7476 (t0) REVERT: A 222 GLU cc_start: 0.7211 (tt0) cc_final: 0.6942 (tt0) REVERT: A 365 ASN cc_start: 0.7838 (p0) cc_final: 0.7109 (p0) REVERT: B 72 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8765 (m-10) REVERT: B 170 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 205 MET cc_start: 0.8955 (mmm) cc_final: 0.8707 (tpt) REVERT: B 225 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6640 (t80) REVERT: C 132 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7726 (p0) REVERT: C 146 MET cc_start: 0.8749 (mtp) cc_final: 0.8438 (mtt) REVERT: C 379 PHE cc_start: 0.8583 (p90) cc_final: 0.8344 (p90) REVERT: D 8 GLU cc_start: 0.8203 (tp30) cc_final: 0.7719 (tp30) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 0.2092 time to fit residues: 52.1302 Evaluate side-chains 160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10539 Z= 0.220 Angle : 0.575 9.722 14265 Z= 0.289 Chirality : 0.043 0.263 1605 Planarity : 0.003 0.024 1735 Dihedral : 7.050 62.226 1408 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % 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: -0.93 (0.24), residues: 1231 helix: -0.06 (0.22), residues: 606 sheet: -0.38 (0.36), residues: 206 loop : -1.37 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 31 HIS 0.006 0.001 HIS D 213 PHE 0.022 0.001 PHE D 72 TYR 0.013 0.001 TYR C 142 ARG 0.002 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8039 (tmm) REVERT: A 222 GLU cc_start: 0.7203 (tt0) cc_final: 0.6935 (tt0) REVERT: A 365 ASN cc_start: 0.7935 (p0) cc_final: 0.7204 (p0) REVERT: B 72 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8800 (m-10) REVERT: B 205 MET cc_start: 0.8962 (mmm) cc_final: 0.8730 (tpt) REVERT: B 225 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6647 (t80) REVERT: C 123 GLU cc_start: 0.5995 (mp0) cc_final: 0.5679 (mp0) REVERT: C 132 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7796 (p0) REVERT: C 146 MET cc_start: 0.8769 (mtp) cc_final: 0.8461 (mtt) REVERT: C 340 PRO cc_start: 0.8967 (Cg_exo) cc_final: 0.8562 (Cg_endo) REVERT: C 379 PHE cc_start: 0.8569 (p90) cc_final: 0.8337 (p90) REVERT: D 8 GLU cc_start: 0.8221 (tp30) cc_final: 0.7719 (tp30) REVERT: D 41 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7167 (mp) REVERT: D 111 LEU cc_start: 0.8953 (tp) cc_final: 0.8617 (tp) outliers start: 33 outliers final: 24 residues processed: 160 average time/residue: 0.2141 time to fit residues: 48.6968 Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0570 chunk 110 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10539 Z= 0.166 Angle : 0.557 9.417 14265 Z= 0.279 Chirality : 0.042 0.213 1605 Planarity : 0.003 0.024 1735 Dihedral : 6.887 58.795 1408 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.68 % Allowed : 19.00 % Favored : 78.32 % 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: -0.80 (0.24), residues: 1231 helix: 0.00 (0.21), residues: 611 sheet: -0.16 (0.37), residues: 193 loop : -1.32 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 31 HIS 0.005 0.001 HIS D 213 PHE 0.019 0.001 PHE C 369 TYR 0.013 0.001 TYR B 150 ARG 0.004 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 148 MET cc_start: 0.8303 (tmm) cc_final: 0.8040 (tmm) REVERT: A 222 GLU cc_start: 0.7169 (tt0) cc_final: 0.6908 (tt0) REVERT: A 365 ASN cc_start: 0.7878 (p0) cc_final: 0.7170 (p0) REVERT: B 72 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: B 205 MET cc_start: 0.8948 (mmm) cc_final: 0.8679 (tpt) REVERT: B 225 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6626 (t80) REVERT: C 123 GLU cc_start: 0.5840 (mp0) cc_final: 0.5496 (mp0) REVERT: C 132 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7672 (p0) REVERT: C 146 MET cc_start: 0.8733 (mtp) cc_final: 0.8456 (mtt) REVERT: C 340 PRO cc_start: 0.8979 (Cg_exo) cc_final: 0.8586 (Cg_endo) REVERT: D 8 GLU cc_start: 0.8162 (tp30) cc_final: 0.7713 (tp30) REVERT: D 41 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7142 (mp) REVERT: D 111 LEU cc_start: 0.8928 (tp) cc_final: 0.8602 (tp) outliers start: 30 outliers final: 25 residues processed: 163 average time/residue: 0.2151 time to fit residues: 50.2738 Evaluate side-chains 167 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.0170 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10539 Z= 0.154 Angle : 0.550 9.987 14265 Z= 0.276 Chirality : 0.042 0.207 1605 Planarity : 0.003 0.024 1735 Dihedral : 6.676 54.469 1408 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.68 % Allowed : 19.00 % Favored : 78.32 % 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 (0.24), residues: 1231 helix: 0.10 (0.22), residues: 607 sheet: -0.02 (0.37), residues: 193 loop : -1.34 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 31 HIS 0.004 0.001 HIS D 213 PHE 0.025 0.001 PHE C 379 TYR 0.013 0.001 TYR C 232 ARG 0.003 0.000 ARG B 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.7141 (tt0) cc_final: 0.6902 (tt0) REVERT: B 72 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8783 (m-10) REVERT: B 225 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6606 (t80) REVERT: C 132 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7552 (p0) REVERT: C 146 MET cc_start: 0.8678 (mtp) cc_final: 0.8400 (mtt) REVERT: C 323 LEU cc_start: 0.8417 (mt) cc_final: 0.8200 (mt) REVERT: C 340 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8676 (Cg_endo) REVERT: D 8 GLU cc_start: 0.8163 (tp30) cc_final: 0.7722 (tp30) REVERT: D 41 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7155 (mp) REVERT: D 111 LEU cc_start: 0.8892 (tp) cc_final: 0.8585 (tp) outliers start: 30 outliers final: 24 residues processed: 163 average time/residue: 0.2084 time to fit residues: 49.2204 Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110758 restraints weight = 14810.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110863 restraints weight = 10213.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112080 restraints weight = 9761.642| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10539 Z= 0.336 Angle : 0.635 10.417 14265 Z= 0.317 Chirality : 0.045 0.207 1605 Planarity : 0.004 0.026 1735 Dihedral : 6.943 60.563 1408 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.94 % Allowed : 19.09 % Favored : 77.97 % 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: -0.85 (0.24), residues: 1231 helix: -0.03 (0.21), residues: 611 sheet: -0.15 (0.37), residues: 195 loop : -1.39 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 31 HIS 0.006 0.001 HIS D 213 PHE 0.022 0.002 PHE C 379 TYR 0.015 0.001 TYR C 142 ARG 0.003 0.001 ARG C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.42 seconds wall clock time: 37 minutes 8.99 seconds (2228.99 seconds total)