Starting phenix.real_space_refine on Fri Feb 16 04:48:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk1_33883/02_2024/7yk1_33883_updated.pdb" } resolution = 3.08 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= 0.011 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 30 5.49 5 Mg 6 5.21 5 S 90 5.16 5 C 8934 2.51 5 N 2496 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14364 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "F" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 2, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.12, per 1000 atoms: 0.50 Number of scatterers: 14364 At special positions: 0 Unit cell: (124.02, 130.38, 77.38, 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 90 16.00 P 30 15.00 Mg 6 11.99 O 2808 8.00 N 2496 7.00 C 8934 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.4 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 18 sheets defined 35.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 228 through 238 removed outlier: 5.649A pdb=" N ALA A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.658A pdb=" N ALA C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 178 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 179 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 180 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 182 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 160 through 164 removed outlier: 4.502A pdb=" N LYS D 163 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.662A pdb=" N ALA D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR D 179 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 182 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'E' and resid 13 through 23 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.811A pdb=" N ALA E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 177 " --> pdb=" O GLY E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 309 through 314 Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 160 through 164 removed outlier: 4.590A pdb=" N LYS F 163 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 185 removed outlier: 3.646A pdb=" N ALA F 175 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 178 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR F 179 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 182 " --> pdb=" O THR F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 238 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 309 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.388A pdb=" N ASP A 52 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 8.267A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 219 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N SER A 169 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.433A pdb=" N ASP B 52 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 8.265A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 244 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 269 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 246 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 271 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 219 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N SER B 169 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.417A pdb=" N ASP C 52 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 8.307A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 244 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 269 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 246 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 271 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL C 219 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N SER C 169 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.412A pdb=" N ASP D 52 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 8.268A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL D 219 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER D 169 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.416A pdb=" N ASP E 52 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 8.320A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 244 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL E 269 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA E 246 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL E 271 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL E 219 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER E 169 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.408A pdb=" N ASP F 52 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 8.351A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 269 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA F 246 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 219 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N SER F 169 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1068 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: 4.00 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4723 1.34 - 1.46: 1766 1.46 - 1.57: 7917 1.57 - 1.69: 36 1.69 - 1.81: 138 Bond restraints: 14580 Sorted by residual: bond pdb=" O3 PO4 A 401 " pdb=" P PO4 A 401 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3 PO4 F 403 " pdb=" P PO4 F 403 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O4 PO4 B 401 " pdb=" P PO4 B 401 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.68e+00 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 99.66 - 107.11: 470 107.11 - 114.56: 9166 114.56 - 122.00: 7114 122.00 - 129.45: 2948 129.45 - 136.90: 108 Bond angle restraints: 19806 Sorted by residual: angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 112.29 108.63 3.66 9.40e-01 1.13e+00 1.51e+01 angle pdb=" C ILE D 229 " pdb=" N CYS D 230 " pdb=" CA CYS D 230 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N THR D 228 " pdb=" CA THR D 228 " pdb=" C THR D 228 " ideal model delta sigma weight residual 110.80 103.53 7.27 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C ASP F 210 " pdb=" N VAL F 211 " pdb=" CA VAL F 211 " ideal model delta sigma weight residual 121.97 126.92 -4.95 1.80e+00 3.09e-01 7.58e+00 angle pdb=" N THR F 228 " pdb=" CA THR F 228 " pdb=" C THR F 228 " ideal model delta sigma weight residual 110.19 106.88 3.31 1.24e+00 6.50e-01 7.13e+00 ... (remaining 19801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 8437 34.40 - 68.80: 289 68.80 - 103.20: 63 103.20 - 137.60: 13 137.60 - 172.01: 12 Dihedral angle restraints: 8814 sinusoidal: 3492 harmonic: 5322 Sorted by residual: dihedral pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" N9 ADP D 401 " pdb=" C4 ADP D 401 " ideal model delta sinusoidal sigma weight residual 91.55 -96.45 -172.01 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2' ADP F 402 " pdb=" C1' ADP F 402 " pdb=" N9 ADP F 402 " pdb=" C4 ADP F 402 " ideal model delta sinusoidal sigma weight residual 91.55 -96.46 -172.00 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2' ADP C 402 " pdb=" C1' ADP C 402 " pdb=" N9 ADP C 402 " pdb=" C4 ADP C 402 " ideal model delta sinusoidal sigma weight residual 91.55 -100.95 -167.50 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 8811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1265 0.031 - 0.062: 664 0.062 - 0.093: 235 0.093 - 0.124: 169 0.124 - 0.155: 19 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CB VAL F 211 " pdb=" CA VAL F 211 " pdb=" CG1 VAL F 211 " pdb=" CG2 VAL F 211 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE C 290 " pdb=" N ILE C 290 " pdb=" C ILE C 290 " pdb=" CB ILE C 290 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB ILE C 229 " pdb=" CA ILE C 229 " pdb=" CG1 ILE C 229 " pdb=" CG2 ILE C 229 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2349 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 213 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASP E 213 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP E 213 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG E 214 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 12 " -0.001 2.00e-02 2.50e+03 1.07e-02 1.72e+00 pdb=" CG HIS F 12 " 0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS F 12 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS F 12 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS F 12 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS F 12 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 12 " 0.002 2.00e-02 2.50e+03 1.01e-02 1.54e+00 pdb=" CG HIS C 12 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS C 12 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS C 12 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 12 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS C 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 170 2.60 - 3.18: 11805 3.18 - 3.75: 21880 3.75 - 4.33: 32984 4.33 - 4.90: 53362 Nonbonded interactions: 120201 Sorted by model distance: nonbonded pdb=" O1A ADP B 404 " pdb="MG MG E 404 " model vdw 2.029 2.170 nonbonded pdb=" O2A ADP A 403 " pdb="MG MG C 404 " model vdw 2.038 2.170 nonbonded pdb="MG MG A 402 " pdb=" O1A ADP C 401 " model vdw 2.090 2.170 nonbonded pdb="MG MG B 402 " pdb=" O2A ADP E 402 " model vdw 2.093 2.170 nonbonded pdb=" O THR B 249 " pdb=" OG1 THR B 272 " model vdw 2.138 2.440 ... (remaining 120196 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 2 through 316) selection = (chain 'B' and resid 2 through 316) selection = (chain 'C' and resid 2 through 316) selection = (chain 'D' and resid 2 through 316) selection = (chain 'E' and resid 2 through 316) selection = (chain 'F' and resid 2 through 316) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 38.870 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14580 Z= 0.396 Angle : 0.690 7.265 19806 Z= 0.325 Chirality : 0.047 0.155 2352 Planarity : 0.004 0.028 2472 Dihedral : 20.078 172.005 5346 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.24 % Favored : 93.98 % Rotamer: Outliers : 0.26 % Allowed : 17.64 % Favored : 82.11 % 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: -1.48 (0.19), residues: 1812 helix: -0.60 (0.19), residues: 690 sheet: -0.65 (0.23), residues: 534 loop : -1.50 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 154 HIS 0.016 0.002 HIS F 12 PHE 0.013 0.002 PHE A 313 TYR 0.011 0.002 TYR B 54 ARG 0.004 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.629 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 191 average time/residue: 0.2726 time to fit residues: 77.0041 Evaluate side-chains 188 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14580 Z= 0.166 Angle : 0.607 6.715 19806 Z= 0.272 Chirality : 0.045 0.129 2352 Planarity : 0.003 0.026 2472 Dihedral : 16.009 174.134 2071 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.68 % Favored : 93.60 % Rotamer: Outliers : 1.74 % Allowed : 17.18 % Favored : 81.07 % 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: -0.73 (0.20), residues: 1812 helix: 0.43 (0.20), residues: 678 sheet: -0.42 (0.24), residues: 534 loop : -1.46 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.006 0.001 HIS F 12 PHE 0.008 0.001 PHE C 138 TYR 0.006 0.001 TYR E 311 ARG 0.005 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.704 Fit side-chains REVERT: A 33 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7992 (ptmt) REVERT: C 32 THR cc_start: 0.8747 (p) cc_final: 0.8483 (m) outliers start: 27 outliers final: 15 residues processed: 215 average time/residue: 0.3034 time to fit residues: 92.5794 Evaluate side-chains 207 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 164 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN F 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14580 Z= 0.482 Angle : 0.740 7.406 19806 Z= 0.344 Chirality : 0.050 0.187 2352 Planarity : 0.004 0.028 2472 Dihedral : 16.069 170.104 2066 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.16 % Rotamer: Outliers : 2.91 % Allowed : 17.25 % 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: -1.00 (0.20), residues: 1812 helix: 0.28 (0.20), residues: 690 sheet: -0.60 (0.23), residues: 534 loop : -1.69 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 154 HIS 0.010 0.002 HIS A 12 PHE 0.014 0.002 PHE A 313 TYR 0.009 0.002 TYR E 311 ARG 0.003 0.001 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.637 Fit side-chains REVERT: A 26 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 26 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7622 (mp0) outliers start: 45 outliers final: 37 residues processed: 213 average time/residue: 0.2768 time to fit residues: 86.3592 Evaluate side-chains 216 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14580 Z= 0.338 Angle : 0.681 7.403 19806 Z= 0.309 Chirality : 0.048 0.142 2352 Planarity : 0.004 0.031 2472 Dihedral : 15.468 179.343 2066 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.96 % Favored : 93.32 % Rotamer: Outliers : 3.10 % Allowed : 17.96 % Favored : 78.94 % 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: -0.93 (0.20), residues: 1812 helix: 0.48 (0.20), residues: 678 sheet: -0.55 (0.23), residues: 534 loop : -1.82 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.008 0.001 HIS A 12 PHE 0.010 0.001 PHE A 313 TYR 0.007 0.001 TYR E 311 ARG 0.002 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 1.822 Fit side-chains REVERT: A 26 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 176 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7971 (mtpp) REVERT: B 176 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7898 (mtpp) REVERT: C 176 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8396 (tttm) REVERT: D 25 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8573 (pp) outliers start: 48 outliers final: 34 residues processed: 215 average time/residue: 0.2786 time to fit residues: 87.1121 Evaluate side-chains 214 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14580 Z= 0.156 Angle : 0.611 7.477 19806 Z= 0.270 Chirality : 0.045 0.162 2352 Planarity : 0.003 0.029 2472 Dihedral : 14.280 173.910 2066 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.02 % Favored : 94.26 % Rotamer: Outliers : 2.45 % Allowed : 18.48 % Favored : 79.07 % 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: -0.46 (0.20), residues: 1812 helix: 0.89 (0.21), residues: 678 sheet: -0.21 (0.24), residues: 522 loop : -1.68 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 162 HIS 0.005 0.001 HIS E 12 PHE 0.007 0.001 PHE C 138 TYR 0.005 0.001 TYR E 311 ARG 0.003 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 1.601 Fit side-chains REVERT: A 176 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7834 (mtpp) REVERT: B 26 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 176 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7788 (mtpp) REVERT: D 25 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8580 (pp) REVERT: D 286 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: E 32 THR cc_start: 0.8644 (p) cc_final: 0.8389 (m) outliers start: 38 outliers final: 27 residues processed: 214 average time/residue: 0.2703 time to fit residues: 84.1328 Evaluate side-chains 219 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 91 optimal weight: 9.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 305 ASN E 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 14580 Z= 0.518 Angle : 0.775 9.008 19806 Z= 0.356 Chirality : 0.051 0.177 2352 Planarity : 0.004 0.028 2472 Dihedral : 14.916 179.913 2066 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.07 % Favored : 93.10 % Rotamer: Outliers : 3.29 % Allowed : 17.51 % Favored : 79.20 % 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: -0.97 (0.20), residues: 1812 helix: 0.42 (0.20), residues: 678 sheet: -0.55 (0.23), residues: 534 loop : -1.85 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 162 HIS 0.011 0.002 HIS A 12 PHE 0.015 0.002 PHE A 313 TYR 0.008 0.002 TYR E 311 ARG 0.003 0.001 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.758 Fit side-chains REVERT: A 26 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 26 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 25 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8538 (pp) REVERT: D 286 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8023 (mttp) REVERT: F 25 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8546 (pp) outliers start: 51 outliers final: 40 residues processed: 210 average time/residue: 0.2657 time to fit residues: 82.2779 Evaluate side-chains 219 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14580 Z= 0.198 Angle : 0.634 6.979 19806 Z= 0.283 Chirality : 0.045 0.128 2352 Planarity : 0.003 0.029 2472 Dihedral : 14.008 171.958 2066 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.72 % Allowed : 4.86 % Favored : 94.43 % Rotamer: Outliers : 2.78 % Allowed : 18.15 % Favored : 79.07 % 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: -0.63 (0.20), residues: 1812 helix: 0.70 (0.21), residues: 684 sheet: -0.38 (0.23), residues: 534 loop : -1.67 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 162 HIS 0.006 0.001 HIS E 12 PHE 0.008 0.001 PHE E 138 TYR 0.006 0.001 TYR E 311 ARG 0.002 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.605 Fit side-chains REVERT: A 26 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 33 LYS cc_start: 0.8311 (ptpt) cc_final: 0.7995 (ptmt) REVERT: A 176 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7879 (mtpp) REVERT: B 26 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 33 LYS cc_start: 0.8336 (ptpt) cc_final: 0.8011 (ptmt) REVERT: B 176 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7887 (mtpp) REVERT: D 25 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8532 (pp) REVERT: D 286 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: F 25 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8530 (pp) outliers start: 43 outliers final: 31 residues processed: 221 average time/residue: 0.2675 time to fit residues: 86.9439 Evaluate side-chains 229 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 136 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14580 Z= 0.142 Angle : 0.607 6.704 19806 Z= 0.267 Chirality : 0.045 0.126 2352 Planarity : 0.003 0.028 2472 Dihedral : 13.510 175.996 2066 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.24 % Favored : 94.04 % Rotamer: Outliers : 2.33 % Allowed : 18.80 % Favored : 78.88 % 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: -0.27 (0.20), residues: 1812 helix: 1.01 (0.21), residues: 678 sheet: -0.07 (0.24), residues: 522 loop : -1.57 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 162 HIS 0.005 0.001 HIS E 12 PHE 0.007 0.001 PHE C 138 TYR 0.003 0.001 TYR B 311 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.620 Fit side-chains REVERT: A 26 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: B 26 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: B 176 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7818 (mtpp) REVERT: C 32 THR cc_start: 0.8664 (p) cc_final: 0.8460 (m) REVERT: D 25 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 286 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8030 (mttp) REVERT: F 25 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8569 (pp) REVERT: F 29 LYS cc_start: 0.8945 (mttp) cc_final: 0.8689 (mttm) outliers start: 36 outliers final: 27 residues processed: 218 average time/residue: 0.2770 time to fit residues: 87.3187 Evaluate side-chains 228 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14580 Z= 0.188 Angle : 0.627 6.654 19806 Z= 0.278 Chirality : 0.045 0.130 2352 Planarity : 0.003 0.027 2472 Dihedral : 13.571 175.376 2064 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.35 % Favored : 93.93 % Rotamer: Outliers : 2.33 % Allowed : 18.86 % Favored : 78.81 % 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: -0.22 (0.21), residues: 1812 helix: 1.02 (0.21), residues: 678 sheet: -0.02 (0.24), residues: 522 loop : -1.53 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 162 HIS 0.005 0.001 HIS E 12 PHE 0.009 0.001 PHE D 138 TYR 0.004 0.001 TYR B 311 ARG 0.002 0.000 ARG F 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.796 Fit side-chains REVERT: B 176 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7895 (mtpp) REVERT: D 25 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8526 (pp) REVERT: D 286 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8029 (mttp) REVERT: E 22 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8583 (mtt180) REVERT: E 186 ASN cc_start: 0.8267 (t0) cc_final: 0.8002 (t0) REVERT: F 25 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8477 (pp) REVERT: F 29 LYS cc_start: 0.8959 (mttp) cc_final: 0.8693 (mttm) outliers start: 36 outliers final: 28 residues processed: 211 average time/residue: 0.2642 time to fit residues: 82.5386 Evaluate side-chains 225 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14580 Z= 0.162 Angle : 0.613 6.721 19806 Z= 0.271 Chirality : 0.045 0.129 2352 Planarity : 0.003 0.028 2472 Dihedral : 13.449 176.432 2064 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.08 % Favored : 94.21 % Rotamer: Outliers : 2.07 % Allowed : 19.25 % 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: -0.15 (0.21), residues: 1812 helix: 1.08 (0.21), residues: 678 sheet: 0.03 (0.24), residues: 522 loop : -1.50 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 162 HIS 0.005 0.001 HIS E 12 PHE 0.008 0.001 PHE D 138 TYR 0.004 0.001 TYR B 311 ARG 0.002 0.000 ARG F 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.501 Fit side-chains REVERT: A 292 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8875 (pt) REVERT: B 176 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7882 (mtpp) REVERT: D 25 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8520 (pp) REVERT: E 186 ASN cc_start: 0.8248 (t0) cc_final: 0.7988 (t0) REVERT: F 25 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8515 (pp) REVERT: F 29 LYS cc_start: 0.8957 (mttp) cc_final: 0.8694 (mttm) outliers start: 32 outliers final: 27 residues processed: 210 average time/residue: 0.2579 time to fit residues: 80.4703 Evaluate side-chains 225 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 228 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.117216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.108717 restraints weight = 15186.850| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 0.39 r_work: 0.2880 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14580 Z= 0.225 Angle : 0.643 6.623 19806 Z= 0.287 Chirality : 0.046 0.135 2352 Planarity : 0.003 0.029 2472 Dihedral : 13.530 174.400 2064 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.52 % Favored : 93.76 % Rotamer: Outliers : 2.33 % Allowed : 19.06 % Favored : 78.62 % 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: -0.26 (0.21), residues: 1812 helix: 0.98 (0.21), residues: 678 sheet: -0.12 (0.24), residues: 534 loop : -1.49 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.006 0.001 HIS A 12 PHE 0.009 0.001 PHE E 138 TYR 0.005 0.001 TYR C 311 ARG 0.006 0.000 ARG F 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.68 seconds wall clock time: 51 minutes 59.91 seconds (3119.91 seconds total)