Starting phenix.real_space_refine on Wed Nov 15 01:56:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/11_2023/7k2t_22644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/11_2023/7k2t_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_22644/11_2023/7k2t_22644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/11_2023/7k2t_22644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/11_2023/7k2t_22644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k2t_22644/11_2023/7k2t_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.87, per 1000 atoms: 0.57 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: 4.12 Conformation dependent library (CDL) restraints added in 1.8 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: 1.81 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: 2.64 Time building geometry restraints manager: 4.42 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: 5523 17.55 - 35.09: 521 35.09 - 52.64: 74 52.64 - 70.19: 18 70.19 - 87.73: 9 Dihedral angle restraints: 6145 sinusoidal: 2509 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 6142 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: 1.340 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: 4.370 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.980 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- 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 : 13.976 87.734 3813 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 *********************** 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 : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2808 time to fit residues: 85.9597 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5119 ------------------------------------------------------------------------------- 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 A 368 ASN B 45 HIS C 189 GLN C 272 ASN C 307 GLN C 313 ASN D 177 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10539 Z= 0.388 Angle : 0.668 9.921 14265 Z= 0.340 Chirality : 0.046 0.155 1605 Planarity : 0.004 0.033 1735 Dihedral : 6.534 85.173 1346 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.59 % Allowed : 12.22 % Favored : 85.19 % 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: -2.34 (0.22), residues: 1231 helix: -1.02 (0.20), residues: 607 sheet: -1.43 (0.35), residues: 183 loop : -2.17 (0.27), residues: 441 *********************** 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 186 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.157 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 174 average time/residue: 0.2336 time to fit residues: 56.3561 Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1123 time to fit residues: 5.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10539 Z= 0.256 Angle : 0.590 9.486 14265 Z= 0.300 Chirality : 0.043 0.162 1605 Planarity : 0.004 0.028 1735 Dihedral : 6.471 84.736 1346 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.78 % Allowed : 14.27 % 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: -1.83 (0.23), residues: 1231 helix: -0.67 (0.21), residues: 607 sheet: -1.10 (0.35), residues: 190 loop : -1.87 (0.27), residues: 434 *********************** 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 170 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.278 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.2385 time to fit residues: 54.2759 Evaluate side-chains 144 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1012 time to fit residues: 3.7751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS C 167 GLN C 199 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2288 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= 0.348 Angle : 0.625 10.393 14265 Z= 0.317 Chirality : 0.044 0.148 1605 Planarity : 0.004 0.029 1735 Dihedral : 6.461 85.086 1346 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.78 % Allowed : 16.32 % Favored : 81.89 % 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: -1.61 (0.23), residues: 1231 helix: -0.55 (0.21), residues: 607 sheet: -0.84 (0.35), residues: 201 loop : -1.74 (0.29), residues: 423 *********************** 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 169 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.214 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 164 average time/residue: 0.2482 time to fit residues: 56.5211 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0909 time to fit residues: 3.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0030 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 365 ASN A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS D 16 ASN D 45 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10539 Z= 0.205 Angle : 0.572 9.991 14265 Z= 0.287 Chirality : 0.042 0.152 1605 Planarity : 0.004 0.027 1735 Dihedral : 6.306 88.834 1346 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.96 % Allowed : 17.04 % Favored : 81.00 % 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: -1.33 (0.24), residues: 1231 helix: -0.31 (0.21), residues: 606 sheet: -0.74 (0.35), residues: 201 loop : -1.61 (0.29), residues: 424 *********************** 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 178 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.177 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 172 average time/residue: 0.2324 time to fit residues: 55.9870 Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0980 time to fit residues: 2.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN D 12 GLN D 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10539 Z= 0.197 Angle : 0.591 9.570 14265 Z= 0.296 Chirality : 0.043 0.224 1605 Planarity : 0.004 0.027 1735 Dihedral : 6.148 88.996 1346 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.87 % Allowed : 17.31 % 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: -1.10 (0.24), residues: 1231 helix: -0.16 (0.22), residues: 599 sheet: -0.69 (0.36), residues: 204 loop : -1.38 (0.29), residues: 428 *********************** 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 177 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 167 average time/residue: 0.2328 time to fit residues: 54.9133 Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1120 time to fit residues: 3.6269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10539 Z= 0.213 Angle : 0.594 11.787 14265 Z= 0.294 Chirality : 0.043 0.185 1605 Planarity : 0.003 0.027 1735 Dihedral : 6.047 87.715 1346 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.62 % Allowed : 18.55 % 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: -0.99 (0.24), residues: 1231 helix: -0.09 (0.22), residues: 599 sheet: -0.65 (0.36), residues: 212 loop : -1.28 (0.30), residues: 420 *********************** 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 156 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.228 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 153 average time/residue: 0.2363 time to fit residues: 50.8711 Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0973 time to fit residues: 2.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.0470 chunk 113 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 365 ASN A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10539 Z= 0.183 Angle : 0.576 10.680 14265 Z= 0.287 Chirality : 0.042 0.170 1605 Planarity : 0.003 0.025 1735 Dihedral : 5.916 86.542 1346 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.62 % Allowed : 19.54 % Favored : 79.84 % 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: -0.87 (0.24), residues: 1231 helix: 0.01 (0.22), residues: 601 sheet: -0.50 (0.36), residues: 207 loop : -1.28 (0.29), residues: 423 *********************** 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 157 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.324 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 153 average time/residue: 0.2287 time to fit residues: 49.7314 Evaluate side-chains 144 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0998 time to fit residues: 2.4761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 107 ASN A 368 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10539 Z= 0.177 Angle : 0.583 10.839 14265 Z= 0.287 Chirality : 0.042 0.161 1605 Planarity : 0.003 0.028 1735 Dihedral : 5.804 84.873 1346 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.71 % Allowed : 19.89 % Favored : 79.39 % 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 (0.24), residues: 1231 helix: 0.01 (0.22), residues: 612 sheet: -0.28 (0.37), residues: 195 loop : -1.30 (0.29), residues: 424 *********************** 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 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.128 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 151 average time/residue: 0.2292 time to fit residues: 49.4912 Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1051 time to fit residues: 2.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10539 Z= 0.208 Angle : 0.587 10.446 14265 Z= 0.290 Chirality : 0.042 0.148 1605 Planarity : 0.003 0.026 1735 Dihedral : 5.754 83.770 1346 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.27 % Allowed : 20.52 % 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: -0.69 (0.24), residues: 1231 helix: 0.11 (0.22), residues: 598 sheet: -0.29 (0.37), residues: 195 loop : -1.18 (0.29), residues: 438 ********************** 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 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.288 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 147 average time/residue: 0.2600 time to fit residues: 53.7848 Evaluate side-chains 137 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0969 time to fit residues: 1.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114136 restraints weight = 14667.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114870 restraints weight = 9318.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116619 restraints weight = 7948.776| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10539 Z= 0.191 Angle : 0.588 11.046 14265 Z= 0.290 Chirality : 0.042 0.147 1605 Planarity : 0.003 0.028 1735 Dihedral : 5.715 82.722 1346 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.45 % Allowed : 20.52 % Favored : 79.04 % 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: -0.65 (0.24), residues: 1231 helix: 0.14 (0.22), residues: 597 sheet: -0.30 (0.37), residues: 195 loop : -1.13 (0.29), residues: 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.50 seconds wall clock time: 39 minutes 0.69 seconds (2340.69 seconds total)