Starting phenix.real_space_refine on Sat Apr 6 19:53:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg1_40450/04_2024/8sg1_40450_updated.pdb" } resolution = 2.94 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= 0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5669 2.51 5 N 1490 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 138": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 3 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.95, per 1000 atoms: 0.56 Number of scatterers: 8846 At special positions: 0 Unit cell: (94.976, 119.568, 125.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1621 8.00 N 1490 7.00 C 5669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 31.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.929A pdb=" N ILE R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 100 removed outlier: 3.557A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 109 through 111 No H-bonds generated for 'chain 'R' and resid 109 through 111' Processing helix chain 'R' and resid 115 through 142 removed outlier: 3.903A pdb=" N PHE R 128 " --> pdb=" O PHE R 124 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 129 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 removed outlier: 3.641A pdb=" N ASN R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 177 Proline residue: R 173 - end of helix removed outlier: 3.921A pdb=" N VAL R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 250 removed outlier: 5.043A pdb=" N VAL R 231 " --> pdb=" O CYS R 227 " (cutoff:3.500A) Proline residue: R 232 - end of helix Processing helix chain 'R' and resid 257 through 285 removed outlier: 3.617A pdb=" N ILE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 275 - end of helix removed outlier: 3.805A pdb=" N LEU R 284 " --> pdb=" O ASN R 280 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N HIS R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 311 removed outlier: 3.758A pdb=" N LEU R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.889A pdb=" N ALA R 307 " --> pdb=" O ALA R 303 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN R 308 " --> pdb=" O LEU R 304 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N CYS R 310 " --> pdb=" O ILE R 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 316 No H-bonds generated for 'chain 'R' and resid 313 through 316' Processing helix chain 'R' and resid 321 through 326 removed outlier: 4.031A pdb=" N PHE R 326 " --> pdb=" O ASP R 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'A' and resid 7 through 29 removed outlier: 3.853A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.276A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 183 Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.866A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.601A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.916A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.474A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.732A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.406A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.794A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 156 through 161 removed outlier: 3.714A pdb=" N VAL E 156 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 244 through 246 removed outlier: 3.864A pdb=" N GLY E 226 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 190 " --> pdb=" O TRP E 177 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1412 1.31 - 1.44: 2497 1.44 - 1.56: 5028 1.56 - 1.69: 2 1.69 - 1.81: 95 Bond restraints: 9034 Sorted by residual: bond pdb=" C CYS R 272 " pdb=" O CYS R 272 " ideal model delta sigma weight residual 1.236 1.325 -0.089 1.15e-02 7.56e+03 5.93e+01 bond pdb=" C THR R 268 " pdb=" O THR R 268 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.15e-02 7.56e+03 3.45e+01 bond pdb=" C TRP R 273 " pdb=" O TRP R 273 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.19e-02 7.06e+03 1.58e+01 bond pdb=" C PHE R 270 " pdb=" O PHE R 270 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.16e-02 7.43e+03 1.47e+01 bond pdb=" C ILE R 266 " pdb=" O ILE R 266 " ideal model delta sigma weight residual 1.237 1.277 -0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 92.15 - 100.64: 13 100.64 - 109.13: 687 109.13 - 117.62: 5989 117.62 - 126.11: 5408 126.11 - 134.60: 134 Bond angle restraints: 12231 Sorted by residual: angle pdb=" CA PRO R 275 " pdb=" N PRO R 275 " pdb=" CD PRO R 275 " ideal model delta sigma weight residual 112.00 92.15 19.85 1.40e+00 5.10e-01 2.01e+02 angle pdb=" N MET R 111 " pdb=" CA MET R 111 " pdb=" C MET R 111 " ideal model delta sigma weight residual 112.88 103.50 9.38 1.29e+00 6.01e-01 5.29e+01 angle pdb=" N VAL R 73 " pdb=" CA VAL R 73 " pdb=" C VAL R 73 " ideal model delta sigma weight residual 113.42 105.36 8.06 1.17e+00 7.31e-01 4.75e+01 angle pdb=" N CYS R 112 " pdb=" CA CYS R 112 " pdb=" C CYS R 112 " ideal model delta sigma weight residual 114.56 106.02 8.54 1.27e+00 6.20e-01 4.52e+01 angle pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " pdb=" CG TYR E 236 " ideal model delta sigma weight residual 113.90 103.37 10.53 1.80e+00 3.09e-01 3.42e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4877 17.47 - 34.94: 408 34.94 - 52.41: 91 52.41 - 69.88: 14 69.88 - 87.34: 7 Dihedral angle restraints: 5397 sinusoidal: 2131 harmonic: 3266 Sorted by residual: dihedral pdb=" C TYR E 236 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual -122.60 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta harmonic sigma weight residual 122.80 144.39 -21.59 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 1375 0.184 - 0.368: 19 0.368 - 0.552: 0 0.552 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA MET R 101 " pdb=" N MET R 101 " pdb=" C MET R 101 " pdb=" CB MET R 101 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA MET R 111 " pdb=" N MET R 111 " pdb=" C MET R 111 " pdb=" CB MET R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1392 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 274 " -0.127 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO R 275 " 0.298 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 271 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C LEU R 271 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU R 271 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS R 272 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 275 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" C PRO R 275 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO R 275 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR R 276 " 0.025 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1531 2.77 - 3.30: 7957 3.30 - 3.83: 14049 3.83 - 4.37: 17146 4.37 - 4.90: 30545 Nonbonded interactions: 71228 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.235 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.246 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR E 151 " pdb=" OE1 GLU E 154 " model vdw 2.263 2.440 nonbonded pdb=" O THR E 145 " pdb=" OG1 THR E 244 " model vdw 2.265 2.440 ... (remaining 71223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.040 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9034 Z= 0.349 Angle : 0.890 19.854 12231 Z= 0.605 Chirality : 0.063 0.921 1395 Planarity : 0.007 0.173 1532 Dihedral : 13.730 87.345 3276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % Favored : 80.73 % Cbeta Deviations : 0.19 % 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: 0.06 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 351 sheet: 0.41 (0.31), residues: 281 loop : -0.79 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 273 HIS 0.013 0.001 HIS B 225 PHE 0.029 0.001 PHE L 154 TYR 0.061 0.002 TYR E 236 ARG 0.009 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo) REVERT: B 197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180) REVERT: E 235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 1.1314 time to fit residues: 156.1431 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 275 PRO Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 74 ASN B 175 GLN B 266 HIS A 331 ASN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9034 Z= 0.150 Angle : 0.517 7.986 12231 Z= 0.268 Chirality : 0.041 0.204 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.901 57.908 1324 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.99 % Allowed : 18.43 % Favored : 79.58 % 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: 0.37 (0.25), residues: 1105 helix: 1.44 (0.29), residues: 362 sheet: 0.47 (0.30), residues: 282 loop : -0.84 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE R 259 TYR 0.017 0.001 TYR E 236 ARG 0.004 0.000 ARG R 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 218 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6535 (ttt) REVERT: B 215 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 261 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8210 (p0) REVERT: E 235 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6628 (mm-30) REVERT: E 236 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5120 (t80) outliers start: 19 outliers final: 5 residues processed: 112 average time/residue: 1.1892 time to fit residues: 142.9803 Evaluate side-chains 101 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 67 optimal weight: 0.3980 chunk 27 optimal weight: 0.0070 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 175 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.109 Angle : 0.466 8.055 12231 Z= 0.239 Chirality : 0.040 0.169 1395 Planarity : 0.003 0.050 1532 Dihedral : 5.089 54.276 1307 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.41 % Allowed : 18.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1105 helix: 1.71 (0.29), residues: 364 sheet: 0.55 (0.31), residues: 263 loop : -0.79 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS E 35 PHE 0.025 0.001 PHE R 169 TYR 0.013 0.001 TYR E 236 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7276 (mtm180) REVERT: B 215 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 48 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7349 (t) REVERT: A 53 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.5564 (mpt) REVERT: A 261 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (p0) REVERT: E 203 ARG cc_start: 0.7396 (mtp180) cc_final: 0.6941 (mtp180) REVERT: E 235 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6621 (mm-30) REVERT: E 236 TYR cc_start: 0.5318 (OUTLIER) cc_final: 0.4713 (t80) REVERT: E 246 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6626 (mp) outliers start: 23 outliers final: 6 residues processed: 125 average time/residue: 1.1346 time to fit residues: 152.2702 Evaluate side-chains 111 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 150 HIS B 175 GLN B 340 ASN G 59 ASN A 52 GLN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9034 Z= 0.412 Angle : 0.637 8.571 12231 Z= 0.329 Chirality : 0.047 0.247 1395 Planarity : 0.005 0.062 1532 Dihedral : 5.834 55.743 1306 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.82 % Allowed : 16.23 % Favored : 78.95 % 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: 0.31 (0.25), residues: 1105 helix: 1.50 (0.29), residues: 360 sheet: 0.35 (0.30), residues: 280 loop : -0.90 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.006 0.001 HIS E 233 PHE 0.022 0.002 PHE R 169 TYR 0.028 0.002 TYR E 236 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6751 (ptt) REVERT: R 271 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 214 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7319 (mtt-85) REVERT: B 215 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 217 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7492 (pmm) REVERT: G 28 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6823 (pp) REVERT: A 53 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.5529 (mpt) REVERT: A 261 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8240 (p0) REVERT: E 203 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7015 (mtp180) REVERT: E 235 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6800 (mm-30) REVERT: E 246 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6826 (mp) outliers start: 46 outliers final: 18 residues processed: 142 average time/residue: 1.0737 time to fit residues: 164.1359 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 88 ASN B 175 GLN B 340 ASN G 59 ASN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 232 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9034 Z= 0.150 Angle : 0.508 7.493 12231 Z= 0.260 Chirality : 0.042 0.193 1395 Planarity : 0.004 0.057 1532 Dihedral : 5.358 55.529 1306 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.04 % Allowed : 18.85 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1105 helix: 1.78 (0.29), residues: 358 sheet: 0.42 (0.30), residues: 283 loop : -0.81 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.014 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 MET cc_start: 0.6975 (ptp) cc_final: 0.6647 (ptt) REVERT: R 271 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6786 (mp) REVERT: B 214 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7312 (mtm180) REVERT: B 215 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 217 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7445 (pmt) REVERT: G 28 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6900 (pp) REVERT: G 47 GLU cc_start: 0.8144 (pt0) cc_final: 0.7854 (pt0) REVERT: A 261 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (p0) REVERT: E 62 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7094 (p0) REVERT: E 203 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7190 (mtp180) REVERT: E 216 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7480 (p) REVERT: E 235 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6696 (mm-30) outliers start: 29 outliers final: 9 residues processed: 128 average time/residue: 1.1376 time to fit residues: 156.2802 Evaluate side-chains 117 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 250 ASN B 88 ASN B 175 GLN B 340 ASN G 59 ASN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9034 Z= 0.365 Angle : 0.624 9.330 12231 Z= 0.321 Chirality : 0.046 0.246 1395 Planarity : 0.005 0.060 1532 Dihedral : 5.831 56.739 1306 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.66 % Allowed : 18.32 % Favored : 78.01 % 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: 0.34 (0.25), residues: 1105 helix: 1.61 (0.29), residues: 360 sheet: 0.29 (0.30), residues: 281 loop : -0.90 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.002 PHE R 169 TYR 0.025 0.002 TYR E 236 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 MET cc_start: 0.7089 (ptp) cc_final: 0.6769 (ptt) REVERT: R 182 ASN cc_start: 0.6482 (OUTLIER) cc_final: 0.6258 (m-40) REVERT: R 271 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6756 (mp) REVERT: B 13 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7280 (tm-30) REVERT: B 214 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.7251 (mtm180) REVERT: B 215 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 217 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7514 (pmm) REVERT: G 28 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6777 (pp) REVERT: A 261 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (p0) REVERT: E 62 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7111 (p0) REVERT: E 203 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7091 (mtp180) REVERT: E 231 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: E 235 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7044 (mt-10) outliers start: 35 outliers final: 19 residues processed: 126 average time/residue: 1.1840 time to fit residues: 159.6830 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN E 82 GLN E 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9034 Z= 0.143 Angle : 0.507 10.455 12231 Z= 0.258 Chirality : 0.041 0.188 1395 Planarity : 0.004 0.055 1532 Dihedral : 5.292 59.220 1306 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.41 % Allowed : 19.58 % Favored : 78.01 % 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: 0.53 (0.25), residues: 1105 helix: 1.75 (0.29), residues: 357 sheet: 0.45 (0.30), residues: 282 loop : -0.81 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR E 236 ARG 0.002 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6643 (ptt) REVERT: R 182 ASN cc_start: 0.6656 (OUTLIER) cc_final: 0.6310 (m110) REVERT: R 271 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 214 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7286 (mtm180) REVERT: B 215 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 217 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7411 (pmt) REVERT: G 28 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6858 (pp) REVERT: G 47 GLU cc_start: 0.8130 (pt0) cc_final: 0.7824 (pt0) REVERT: A 261 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8224 (p0) REVERT: E 62 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7164 (p0) REVERT: E 235 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6815 (mt-10) outliers start: 23 outliers final: 10 residues processed: 122 average time/residue: 1.1778 time to fit residues: 154.1661 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN B 340 ASN G 59 ASN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9034 Z= 0.205 Angle : 0.535 10.763 12231 Z= 0.271 Chirality : 0.042 0.197 1395 Planarity : 0.004 0.056 1532 Dihedral : 5.321 58.962 1306 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.93 % Allowed : 19.58 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1105 helix: 1.84 (0.29), residues: 356 sheet: 0.46 (0.30), residues: 281 loop : -0.80 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 77 HIS 0.004 0.001 HIS E 35 PHE 0.027 0.001 PHE R 169 TYR 0.019 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6625 (ptt) REVERT: R 182 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6290 (m110) REVERT: R 271 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6760 (mp) REVERT: B 214 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7278 (mtm180) REVERT: B 215 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 217 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7430 (pmm) REVERT: G 28 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6857 (pp) REVERT: A 261 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (p0) REVERT: E 62 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7083 (p0) REVERT: E 235 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6905 (mt-10) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 1.1605 time to fit residues: 153.3787 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 175 GLN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9034 Z= 0.127 Angle : 0.498 11.211 12231 Z= 0.250 Chirality : 0.041 0.171 1395 Planarity : 0.003 0.053 1532 Dihedral : 5.014 57.224 1306 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.41 % Allowed : 20.31 % Favored : 77.28 % 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: 0.67 (0.26), residues: 1105 helix: 1.89 (0.29), residues: 357 sheet: 0.52 (0.31), residues: 283 loop : -0.73 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR E 236 ARG 0.001 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.995 Fit side-chains REVERT: R 123 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6596 (ptt) REVERT: R 182 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.5829 (m110) REVERT: B 214 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7272 (mtt-85) REVERT: B 215 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 217 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7423 (pmt) REVERT: G 28 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6893 (pp) REVERT: A 261 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (p0) REVERT: E 235 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6641 (mm-30) outliers start: 23 outliers final: 12 residues processed: 122 average time/residue: 1.1594 time to fit residues: 151.7305 Evaluate side-chains 118 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN B 340 ASN G 59 ASN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9034 Z= 0.230 Angle : 0.554 14.424 12231 Z= 0.279 Chirality : 0.043 0.198 1395 Planarity : 0.004 0.057 1532 Dihedral : 5.228 58.353 1305 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.88 % Allowed : 20.73 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1105 helix: 1.87 (0.29), residues: 357 sheet: 0.50 (0.30), residues: 281 loop : -0.75 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.004 0.001 HIS E 35 PHE 0.029 0.001 PHE R 169 TYR 0.018 0.001 TYR E 236 ARG 0.002 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: R 123 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6632 (ptt) REVERT: R 182 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.5816 (m110) REVERT: B 214 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7274 (mtt-85) REVERT: B 215 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 217 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7423 (pmm) REVERT: G 28 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6869 (pp) REVERT: A 261 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8218 (p0) REVERT: E 235 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6901 (mt-10) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 1.1638 time to fit residues: 147.1305 Evaluate side-chains 118 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 250 ASN B 88 ASN B 175 GLN A 304 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106990 restraints weight = 10455.959| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.32 r_work: 0.3047 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9034 Z= 0.142 Angle : 0.510 13.233 12231 Z= 0.256 Chirality : 0.041 0.175 1395 Planarity : 0.004 0.053 1532 Dihedral : 5.007 57.318 1305 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.20 % Allowed : 20.63 % Favored : 77.17 % 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: 0.70 (0.26), residues: 1105 helix: 1.91 (0.29), residues: 358 sheet: 0.57 (0.31), residues: 280 loop : -0.73 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 77 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 68 TYR 0.012 0.001 TYR E 236 ARG 0.001 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.74 seconds wall clock time: 60 minutes 47.87 seconds (3647.87 seconds total)