Starting phenix.real_space_refine on Thu Feb 15 10:42:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7q_28907/02_2024/8f7q_28907_updated.pdb" } resolution = 3.22 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= 0.009 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 100 5.16 5 C 7797 2.51 5 N 1949 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Residue "M ARG 350": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 437 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1788 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "M" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2312 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 8.55, per 1000 atoms: 0.71 Number of scatterers: 11994 At special positions: 0 Unit cell: (111.384, 112.455, 152.082, 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 100 16.00 O 2148 8.00 N 1949 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " 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: 4.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 15 sheets defined 45.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'R' and resid 67 through 97 Processing helix chain 'R' and resid 104 through 121 Processing helix chain 'R' and resid 123 through 132 Processing helix chain 'R' and resid 139 through 172 Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.597A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.080A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 5.177A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 338 removed outlier: 3.858A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 Processing helix chain 'P' and resid 13 through 20 Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.650A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) 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 280 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.531A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 44 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 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'M' and resid 67 through 97 Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.909A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.619A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.795A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.811A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix Processing helix chain 'M' and resid 227 through 263 removed outlier: 5.087A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix removed outlier: 3.652A pdb=" N SER M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 339 removed outlier: 3.874A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'Q' and resid 13 through 20 Processing helix chain 'F' and resid 337 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.891A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.758A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.611A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.722A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.833A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.841A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.776A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.621A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.924A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 156 through 160 Processing sheet with id= N, first strand: chain 'E' and resid 226 through 232 removed outlier: 5.919A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG E 181 " --> pdb=" O PRO E 186 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 208 through 213 637 hydrogen bonds defined for protein. 1860 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: 3.70 Time building geometry restraints manager: 5.14 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: 3659 1.34 - 1.46: 2776 1.46 - 1.58: 5694 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 12278 Sorted by residual: bond pdb=" C ASN R 334 " pdb=" N PRO R 335 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C LEU M 202 " pdb=" N PRO M 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.50e+00 bond pdb=" C LEU R 202 " pdb=" N PRO R 203 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.36e-02 5.41e+03 3.85e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.49e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.33e+00 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 334 106.42 - 113.33: 6878 113.33 - 120.25: 4319 120.25 - 127.16: 5039 127.16 - 134.08: 133 Bond angle restraints: 16703 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.02 131.81 -6.79 1.76e+00 3.23e-01 1.49e+01 angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 117.47 -7.66 2.21e+00 2.05e-01 1.20e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.82 130.67 -5.85 1.78e+00 3.16e-01 1.08e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 125.66 131.62 -5.96 1.85e+00 2.92e-01 1.04e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 124.82 130.46 -5.64 1.78e+00 3.16e-01 1.00e+01 ... (remaining 16698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 7365 14.13 - 28.27: 321 28.27 - 42.40: 55 42.40 - 56.53: 4 56.53 - 70.67: 3 Dihedral angle restraints: 7748 sinusoidal: 3414 harmonic: 4334 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1709 0.082 - 0.165: 192 0.165 - 0.247: 31 0.247 - 0.330: 10 0.330 - 0.412: 11 Chirality restraints: 1953 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR M 405 " pdb=" C13 CLR M 405 " pdb=" C15 CLR M 405 " pdb=" C8 CLR M 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C14 CLR M 402 " pdb=" C13 CLR M 402 " pdb=" C15 CLR M 402 " pdb=" C8 CLR M 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 1950 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL M 336 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C VAL M 336 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL M 336 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU M 337 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO B 236 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 219 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG E 219 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG E 219 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 220 " 0.011 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2283 2.79 - 3.32: 10970 3.32 - 3.84: 19468 3.84 - 4.37: 21844 4.37 - 4.90: 39479 Nonbonded interactions: 94044 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.262 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.276 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.314 2.440 nonbonded pdb=" O ILE M 292 " pdb=" OG1 THR M 296 " model vdw 2.360 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 219 " model vdw 2.360 2.440 ... (remaining 94039 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 'M' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 4.150 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: 4.170 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 39.040 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.004 0.063 12278 Z= 0.283 Angle : 0.868 9.050 16703 Z= 0.475 Chirality : 0.065 0.412 1953 Planarity : 0.006 0.050 2013 Dihedral : 8.264 70.668 4937 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.89 (0.20), residues: 1462 helix: 1.88 (0.17), residues: 668 sheet: 0.50 (0.30), residues: 283 loop : -1.10 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 111 HIS 0.006 0.001 HIS E 35 PHE 0.032 0.002 PHE Q 18 TYR 0.028 0.002 TYR R 301 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.8330 (mtp) cc_final: 0.8119 (mtp) REVERT: E 159 SER cc_start: 0.8060 (t) cc_final: 0.7788 (p) REVERT: E 187 GLN cc_start: 0.8014 (pt0) cc_final: 0.7788 (pt0) REVERT: M 257 MET cc_start: 0.7689 (ttt) cc_final: 0.7365 (ttt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2765 time to fit residues: 88.7224 Evaluate side-chains 149 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 190 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 75 GLN B 91 HIS B 230 ASN B 237 ASN B 266 HIS E 180 GLN ** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.003 0.047 12278 Z= 0.175 Angle : 0.481 6.962 16703 Z= 0.250 Chirality : 0.038 0.151 1953 Planarity : 0.004 0.049 2013 Dihedral : 5.241 56.657 2256 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.70 % Allowed : 6.40 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.99 (0.21), residues: 1462 helix: 2.92 (0.18), residues: 687 sheet: 0.75 (0.30), residues: 285 loop : -0.73 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS E 233 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR M 151 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: R 163 MET cc_start: 0.8334 (mtp) cc_final: 0.8071 (mtp) REVERT: R 251 THR cc_start: 0.9056 (m) cc_final: 0.8849 (m) REVERT: B 154 ASP cc_start: 0.8151 (m-30) cc_final: 0.7925 (m-30) REVERT: C 38 MET cc_start: 0.7241 (mmm) cc_final: 0.6888 (mmm) REVERT: E 167 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8335 (tt) REVERT: E 187 GLN cc_start: 0.8128 (pt0) cc_final: 0.7919 (pt0) REVERT: M 341 LEU cc_start: 0.7677 (mm) cc_final: 0.7233 (tt) outliers start: 22 outliers final: 13 residues processed: 173 average time/residue: 0.2342 time to fit residues: 58.5707 Evaluate side-chains 151 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 239 ASN B 340 ASN E 82 GLN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7741 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12278 Z= 0.158 Angle : 0.459 5.382 16703 Z= 0.240 Chirality : 0.038 0.151 1953 Planarity : 0.004 0.042 2013 Dihedral : 4.982 53.943 2256 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.16 % Allowed : 6.71 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1462 helix: 3.19 (0.18), residues: 685 sheet: 0.70 (0.30), residues: 284 loop : -0.62 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.008 0.001 PHE P 4 TYR 0.018 0.001 TYR A 230 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.6907 (mmm) cc_final: 0.6680 (mmm) REVERT: R 163 MET cc_start: 0.8360 (mtp) cc_final: 0.8123 (mtp) REVERT: A 230 TYR cc_start: 0.7637 (p90) cc_final: 0.7275 (p90) REVERT: B 198 LEU cc_start: 0.8569 (mp) cc_final: 0.8285 (mt) REVERT: E 141 MET cc_start: 0.8622 (mmm) cc_final: 0.8161 (mmt) REVERT: E 180 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: E 187 GLN cc_start: 0.8187 (pt0) cc_final: 0.7940 (pt0) REVERT: M 341 LEU cc_start: 0.7742 (mm) cc_final: 0.7408 (tt) outliers start: 28 outliers final: 14 residues processed: 158 average time/residue: 0.2226 time to fit residues: 51.8888 Evaluate side-chains 149 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12278 Z= 0.201 Angle : 0.492 6.681 16703 Z= 0.255 Chirality : 0.039 0.163 1953 Planarity : 0.004 0.040 2013 Dihedral : 5.230 53.282 2256 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.01 % Allowed : 8.10 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1462 helix: 3.16 (0.18), residues: 681 sheet: 0.63 (0.30), residues: 279 loop : -0.63 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS E 233 PHE 0.010 0.001 PHE E 240 TYR 0.016 0.002 TYR E 94 ARG 0.004 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: R 74 MET cc_start: 0.6784 (mmm) cc_final: 0.6573 (mmm) REVERT: R 147 SER cc_start: 0.8308 (t) cc_final: 0.8052 (m) REVERT: R 163 MET cc_start: 0.8376 (mtp) cc_final: 0.8139 (mtp) REVERT: R 218 ASP cc_start: 0.7570 (m-30) cc_final: 0.7317 (p0) REVERT: A 193 ASP cc_start: 0.7229 (t0) cc_final: 0.6831 (t0) REVERT: A 230 TYR cc_start: 0.7915 (p90) cc_final: 0.7617 (p90) REVERT: C 37 LEU cc_start: 0.7507 (mp) cc_final: 0.7253 (mp) REVERT: E 87 ARG cc_start: 0.6986 (ttm110) cc_final: 0.6785 (ttm-80) REVERT: E 159 SER cc_start: 0.8247 (t) cc_final: 0.8022 (p) REVERT: M 310 ILE cc_start: 0.7784 (pt) cc_final: 0.7523 (mt) REVERT: M 341 LEU cc_start: 0.7643 (mm) cc_final: 0.7287 (tt) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.2218 time to fit residues: 51.4147 Evaluate side-chains 152 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 187 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12278 Z= 0.273 Angle : 0.527 8.319 16703 Z= 0.273 Chirality : 0.040 0.161 1953 Planarity : 0.004 0.044 2013 Dihedral : 5.660 59.870 2256 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.01 % Allowed : 9.65 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.88 (0.21), residues: 1462 helix: 2.88 (0.18), residues: 678 sheet: 0.49 (0.30), residues: 282 loop : -0.64 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS R 321 PHE 0.014 0.001 PHE B 199 TYR 0.021 0.002 TYR E 94 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.419 Fit side-chains REVERT: R 163 MET cc_start: 0.8473 (mtp) cc_final: 0.8193 (mtp) REVERT: R 218 ASP cc_start: 0.7659 (m-30) cc_final: 0.7453 (p0) REVERT: R 328 TYR cc_start: 0.8696 (m-80) cc_final: 0.8469 (m-80) REVERT: A 230 TYR cc_start: 0.8179 (p90) cc_final: 0.7959 (p90) REVERT: B 70 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8849 (pt) REVERT: C 37 LEU cc_start: 0.7702 (mp) cc_final: 0.7361 (mp) REVERT: E 34 MET cc_start: 0.8169 (mmt) cc_final: 0.7926 (mmt) REVERT: E 87 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6866 (ttm-80) REVERT: E 159 SER cc_start: 0.8293 (t) cc_final: 0.8087 (p) REVERT: M 341 LEU cc_start: 0.7794 (mm) cc_final: 0.7301 (tt) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.2361 time to fit residues: 55.8597 Evaluate side-chains 157 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 187 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12278 Z= 0.149 Angle : 0.463 9.228 16703 Z= 0.237 Chirality : 0.037 0.139 1953 Planarity : 0.003 0.038 2013 Dihedral : 5.379 59.191 2256 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.47 % Allowed : 10.73 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1462 helix: 3.05 (0.18), residues: 680 sheet: 0.58 (0.30), residues: 281 loop : -0.57 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS R 321 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR M 151 ARG 0.002 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.398 Fit side-chains REVERT: R 163 MET cc_start: 0.8395 (mtp) cc_final: 0.8129 (mtp) REVERT: R 205 MET cc_start: 0.8677 (ttm) cc_final: 0.8468 (ttp) REVERT: C 37 LEU cc_start: 0.7688 (mp) cc_final: 0.7431 (mp) REVERT: C 38 MET cc_start: 0.7221 (mmm) cc_final: 0.6876 (mmm) REVERT: E 87 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6848 (ttm-80) REVERT: M 341 LEU cc_start: 0.7679 (mm) cc_final: 0.7265 (tt) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.2358 time to fit residues: 54.1355 Evaluate side-chains 153 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN M 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12278 Z= 0.419 Angle : 0.611 9.951 16703 Z= 0.312 Chirality : 0.043 0.155 1953 Planarity : 0.004 0.044 2013 Dihedral : 6.226 59.687 2256 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.39 % Allowed : 9.65 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.55 (0.21), residues: 1462 helix: 2.53 (0.18), residues: 680 sheet: 0.38 (0.30), residues: 287 loop : -0.72 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS E 233 PHE 0.012 0.002 PHE R 239 TYR 0.030 0.002 TYR E 94 ARG 0.005 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.251 Fit side-chains REVERT: R 163 MET cc_start: 0.8525 (mtp) cc_final: 0.8262 (mtp) REVERT: B 70 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8820 (pt) REVERT: M 211 LYS cc_start: 0.8106 (mttt) cc_final: 0.7904 (mttp) REVERT: M 341 LEU cc_start: 0.7987 (mm) cc_final: 0.7388 (tt) outliers start: 31 outliers final: 25 residues processed: 163 average time/residue: 0.2398 time to fit residues: 56.5935 Evaluate side-chains 159 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12278 Z= 0.177 Angle : 0.478 8.143 16703 Z= 0.249 Chirality : 0.038 0.142 1953 Planarity : 0.004 0.041 2013 Dihedral : 5.521 58.531 2256 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.70 % Allowed : 11.03 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.77 (0.21), residues: 1462 helix: 2.77 (0.19), residues: 678 sheet: 0.51 (0.30), residues: 280 loop : -0.71 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR E 94 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.314 Fit side-chains REVERT: R 163 MET cc_start: 0.8444 (mtp) cc_final: 0.8185 (mtp) REVERT: B 70 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8823 (pt) REVERT: E 87 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6868 (ttm-80) REVERT: M 341 LEU cc_start: 0.7856 (mm) cc_final: 0.7361 (tt) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.2308 time to fit residues: 52.3254 Evaluate side-chains 149 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN M 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12278 Z= 0.152 Angle : 0.461 9.939 16703 Z= 0.238 Chirality : 0.038 0.140 1953 Planarity : 0.003 0.040 2013 Dihedral : 5.268 57.332 2256 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.70 % Allowed : 10.65 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.22), residues: 1462 helix: 2.97 (0.19), residues: 680 sheet: 0.67 (0.30), residues: 282 loop : -0.62 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR R 151 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.431 Fit side-chains REVERT: R 163 MET cc_start: 0.8410 (mtp) cc_final: 0.8127 (mtp) REVERT: B 70 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8835 (pt) REVERT: E 87 ARG cc_start: 0.7207 (ttm110) cc_final: 0.6879 (ttm-80) REVERT: M 341 LEU cc_start: 0.7894 (mm) cc_final: 0.7307 (tt) outliers start: 22 outliers final: 21 residues processed: 155 average time/residue: 0.2226 time to fit residues: 51.3929 Evaluate side-chains 155 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12278 Z= 0.315 Angle : 0.557 12.158 16703 Z= 0.283 Chirality : 0.040 0.149 1953 Planarity : 0.004 0.042 2013 Dihedral : 5.838 58.193 2256 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 10.80 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1462 helix: 2.64 (0.19), residues: 686 sheet: 0.35 (0.30), residues: 284 loop : -0.67 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS E 233 PHE 0.011 0.001 PHE B 241 TYR 0.024 0.002 TYR E 94 ARG 0.007 0.001 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.339 Fit side-chains REVERT: R 163 MET cc_start: 0.8519 (mtp) cc_final: 0.8271 (mtp) REVERT: B 70 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8789 (pt) REVERT: M 341 LEU cc_start: 0.7909 (mm) cc_final: 0.7335 (tt) outliers start: 21 outliers final: 19 residues processed: 143 average time/residue: 0.2323 time to fit residues: 48.8467 Evaluate side-chains 145 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 164 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.161215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124686 restraints weight = 12827.703| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.15 r_work: 0.3019 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12278 Z= 0.182 Angle : 0.488 11.291 16703 Z= 0.249 Chirality : 0.038 0.143 1953 Planarity : 0.004 0.044 2013 Dihedral : 5.472 56.723 2256 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.77 % Allowed : 10.88 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.80 (0.21), residues: 1462 helix: 2.79 (0.19), residues: 684 sheet: 0.48 (0.30), residues: 275 loop : -0.68 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 321 PHE 0.012 0.001 PHE B 241 TYR 0.014 0.001 TYR E 94 ARG 0.008 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2610.26 seconds wall clock time: 48 minutes 53.75 seconds (2933.75 seconds total)