Starting phenix.real_space_refine on Thu Feb 15 08:39:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef6_28069/02_2024/8ef6_28069_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7605 2.51 5 N 1895 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 213": "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 "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 213": "NH1" <-> "NH2" Residue "M ARG 260": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 282": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11686 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} 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: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 428 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {'CLR': 5, 'MOI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {'CLR': 5, 'MOI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.94, per 1000 atoms: 0.51 Number of scatterers: 11686 At special positions: 0 Unit cell: (113.526, 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 98 16.00 O 2088 8.00 N 1895 7.00 C 7605 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=2.03 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: 4.17 Conformation dependent library (CDL) restraints added in 2.2 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 15 sheets defined 45.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'R' and resid 67 through 97 Processing helix chain 'R' and resid 104 through 132 removed outlier: 4.055A pdb=" N THR R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.571A pdb=" N PHE R 154 " --> pdb=" O TYR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.879A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 3.661A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.224A 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: 5.194A 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: 4.031A 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 'A' and resid 7 through 32 removed outlier: 3.854A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) 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: 4.844A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 4.476A 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 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.836A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.511A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) 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 43 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 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'M' and resid 67 through 97 Processing helix chain 'M' and resid 104 through 132 removed outlier: 4.054A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 4.386A 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: 3.572A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.878A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.660A pdb=" N ALA M 199 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 4.224A 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: 5.195A pdb=" N MET M 245 " --> pdb=" O PHE M 241 " (cutoff:3.500A) Proline residue: M 246 - end of helix Processing helix chain 'M' and resid 271 through 307 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 4.031A 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 'F' and resid 337 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 removed outlier: 3.658A pdb=" N THR R 220 " --> pdb=" O THR R 209 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.735A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.919A 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: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.768A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.946A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.772A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A 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: 6.540A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.153A 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: 3.728A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.577A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.729A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.023A 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 227 through 232 removed outlier: 6.171A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 208 through 213 removed outlier: 3.659A pdb=" N THR M 220 " --> pdb=" O THR M 209 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1764 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: 3.48 Time building geometry restraints manager: 4.50 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: 3533 1.34 - 1.46: 2481 1.46 - 1.58: 5811 1.58 - 1.70: 0 1.70 - 1.82: 145 Bond restraints: 11970 Sorted by residual: bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.26e+00 bond pdb=" C THR M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.11e+00 bond pdb=" CA THR R 296 " pdb=" C THR R 296 " ideal model delta sigma weight residual 1.522 1.545 -0.024 1.26e-02 6.30e+03 3.50e+00 bond pdb=" CA THR M 296 " pdb=" C THR M 296 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.26e-02 6.30e+03 3.37e+00 bond pdb=" C MET M 245 " pdb=" N PRO M 246 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.26e+00 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.11: 176 104.11 - 111.60: 5438 111.60 - 119.09: 4407 119.09 - 126.58: 6111 126.58 - 134.07: 171 Bond angle restraints: 16303 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 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH2 ARG B 314 " ideal model delta sigma weight residual 119.20 122.35 -3.15 9.00e-01 1.23e+00 1.22e+01 angle pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH1 ARG B 314 " ideal model delta sigma weight residual 121.50 118.39 3.11 1.00e+00 1.00e+00 9.70e+00 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 125.02 130.40 -5.38 1.76e+00 3.23e-01 9.34e+00 ... (remaining 16298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.93: 6932 10.93 - 21.87: 585 21.87 - 32.80: 85 32.80 - 43.73: 26 43.73 - 54.67: 6 Dihedral angle restraints: 7634 sinusoidal: 3427 harmonic: 4207 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 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 163.57 16.43 0 5.00e+00 4.00e-02 1.08e+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 67.23 25.77 1 1.00e+01 1.00e-02 9.55e+00 ... (remaining 7631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1705 0.089 - 0.177: 169 0.177 - 0.266: 16 0.266 - 0.354: 10 0.354 - 0.443: 10 Chirality restraints: 1910 Sorted by residual: 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 -2.76 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" C14 CLR R 406 " pdb=" C13 CLR R 406 " pdb=" C15 CLR R 406 " pdb=" C8 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 1907 not shown) Planarity restraints: 1958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 236 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 240 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ILE M 240 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE M 240 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE M 241 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 240 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C ILE R 240 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE R 240 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE R 241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1955 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2472 2.79 - 3.32: 10524 3.32 - 3.85: 19008 3.85 - 4.37: 21450 4.37 - 4.90: 38581 Nonbonded interactions: 92035 Sorted by model distance: nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.267 2.440 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.268 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.307 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.308 2.440 ... (remaining 92030 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' } 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.090 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.630 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 0.055 11970 Z= 0.301 Angle : 0.866 10.377 16303 Z= 0.458 Chirality : 0.066 0.443 1910 Planarity : 0.007 0.071 1958 Dihedral : 8.207 54.668 4905 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.00 (0.19), residues: 1421 helix: 0.80 (0.16), residues: 656 sheet: 0.33 (0.30), residues: 274 loop : -1.22 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 332 HIS 0.007 0.001 HIS E 35 PHE 0.024 0.002 PHE M 349 TYR 0.023 0.002 TYR M 108 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: R 166 ASP cc_start: 0.7706 (t0) cc_final: 0.7482 (t0) REVERT: R 211 LYS cc_start: 0.7415 (pttt) cc_final: 0.6989 (ptmm) REVERT: R 260 ARG cc_start: 0.7276 (tpt90) cc_final: 0.6575 (tpp80) REVERT: R 283 MET cc_start: 0.7108 (tpt) cc_final: 0.6799 (mtt) REVERT: R 304 ILE cc_start: 0.8048 (mt) cc_final: 0.7848 (mt) REVERT: A 195 HIS cc_start: 0.7890 (m-70) cc_final: 0.7590 (m-70) REVERT: C 21 MET cc_start: 0.4985 (ttm) cc_final: 0.4435 (tpp) REVERT: E 187 GLN cc_start: 0.7090 (pt0) cc_final: 0.6826 (pt0) REVERT: E 216 THR cc_start: 0.7095 (p) cc_final: 0.6831 (t) REVERT: M 164 SER cc_start: 0.8499 (t) cc_final: 0.8189 (p) REVERT: M 206 PHE cc_start: 0.7636 (m-80) cc_final: 0.7394 (m-80) REVERT: M 232 ASN cc_start: 0.7650 (m110) cc_final: 0.7352 (m-40) REVERT: M 241 PHE cc_start: 0.8172 (m-10) cc_final: 0.7903 (m-80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2429 time to fit residues: 96.6604 Evaluate side-chains 189 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 331 ASN B 91 HIS B 183 HIS B 220 GLN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 ASN M 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11970 Z= 0.240 Angle : 0.554 6.246 16303 Z= 0.289 Chirality : 0.041 0.163 1910 Planarity : 0.005 0.059 1958 Dihedral : 5.579 59.987 2305 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.31 % Allowed : 6.36 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.38 (0.21), residues: 1421 helix: 2.37 (0.18), residues: 658 sheet: 0.48 (0.31), residues: 275 loop : -0.87 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.011 0.002 HIS B 54 PHE 0.016 0.002 PHE A 189 TYR 0.015 0.002 TYR R 108 ARG 0.006 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: R 260 ARG cc_start: 0.7297 (tpt90) cc_final: 0.6592 (tpp80) REVERT: A 18 MET cc_start: 0.7964 (mtp) cc_final: 0.7711 (mtp) REVERT: A 316 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 21 MET cc_start: 0.4940 (ttm) cc_final: 0.4293 (tpp) REVERT: E 187 GLN cc_start: 0.7284 (pt0) cc_final: 0.6926 (pt0) REVERT: M 67 MET cc_start: 0.6002 (tmm) cc_final: 0.5443 (tpp) REVERT: M 77 TYR cc_start: 0.7536 (m-10) cc_final: 0.7290 (m-80) REVERT: M 206 PHE cc_start: 0.7840 (m-80) cc_final: 0.7562 (m-80) REVERT: M 241 PHE cc_start: 0.8306 (m-10) cc_final: 0.8064 (m-80) REVERT: M 257 MET cc_start: 0.8754 (ttp) cc_final: 0.8494 (ttt) outliers start: 29 outliers final: 22 residues processed: 210 average time/residue: 0.2412 time to fit residues: 72.2275 Evaluate side-chains 188 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11970 Z= 0.147 Angle : 0.465 5.486 16303 Z= 0.243 Chirality : 0.038 0.143 1910 Planarity : 0.004 0.053 1958 Dihedral : 5.209 57.924 2305 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 9.46 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.92 (0.21), residues: 1421 helix: 2.88 (0.18), residues: 662 sheet: 0.63 (0.31), residues: 276 loop : -0.68 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 320 HIS 0.005 0.001 HIS B 54 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR E 94 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: R 260 ARG cc_start: 0.7242 (tpt90) cc_final: 0.6551 (tpp80) REVERT: A 33 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6721 (mm-30) REVERT: A 316 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (p) REVERT: C 21 MET cc_start: 0.5234 (ttm) cc_final: 0.4552 (tpp) REVERT: E 187 GLN cc_start: 0.7300 (pt0) cc_final: 0.6977 (pt0) REVERT: M 67 MET cc_start: 0.5813 (tmm) cc_final: 0.5388 (tpp) REVERT: M 77 TYR cc_start: 0.7469 (m-10) cc_final: 0.7114 (m-80) REVERT: M 132 MET cc_start: 0.7060 (mtm) cc_final: 0.6794 (mtp) REVERT: M 205 MET cc_start: 0.7668 (ttt) cc_final: 0.7278 (tpp) REVERT: M 206 PHE cc_start: 0.7685 (m-80) cc_final: 0.7406 (m-80) REVERT: M 241 PHE cc_start: 0.8310 (m-10) cc_final: 0.8046 (m-80) outliers start: 19 outliers final: 16 residues processed: 186 average time/residue: 0.2406 time to fit residues: 64.6642 Evaluate side-chains 176 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN M 173 HIS M 190 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11970 Z= 0.286 Angle : 0.570 7.005 16303 Z= 0.293 Chirality : 0.042 0.204 1910 Planarity : 0.004 0.059 1958 Dihedral : 5.454 46.332 2305 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.10 % Allowed : 9.46 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.70 (0.22), residues: 1421 helix: 2.70 (0.19), residues: 660 sheet: 0.29 (0.29), residues: 290 loop : -0.61 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS B 54 PHE 0.016 0.002 PHE A 189 TYR 0.025 0.002 TYR E 94 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.350 Fit side-chains REVERT: R 102 LYS cc_start: 0.7040 (ptpt) cc_final: 0.6805 (mtmt) REVERT: R 205 MET cc_start: 0.8252 (ttp) cc_final: 0.7986 (ttp) REVERT: R 260 ARG cc_start: 0.7385 (tpt90) cc_final: 0.6660 (tpp80) REVERT: A 33 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: A 255 ASN cc_start: 0.8542 (m-40) cc_final: 0.8205 (m-40) REVERT: A 316 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (p) REVERT: B 138 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 197 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6321 (mpt90) REVERT: C 21 MET cc_start: 0.5364 (ttm) cc_final: 0.4613 (tpp) REVERT: E 63 THR cc_start: 0.7258 (p) cc_final: 0.6974 (p) REVERT: E 187 GLN cc_start: 0.7501 (pt0) cc_final: 0.7137 (pt0) REVERT: M 67 MET cc_start: 0.5943 (tmm) cc_final: 0.5604 (tpp) REVERT: M 206 PHE cc_start: 0.7792 (m-80) cc_final: 0.7586 (m-80) REVERT: M 245 MET cc_start: 0.7728 (mmp) cc_final: 0.7137 (mmp) outliers start: 39 outliers final: 28 residues processed: 201 average time/residue: 0.2432 time to fit residues: 69.7547 Evaluate side-chains 189 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11970 Z= 0.181 Angle : 0.480 6.143 16303 Z= 0.251 Chirality : 0.039 0.138 1910 Planarity : 0.004 0.051 1958 Dihedral : 5.044 55.058 2305 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.38 % Allowed : 11.29 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1421 helix: 2.86 (0.19), residues: 660 sheet: 0.19 (0.29), residues: 293 loop : -0.49 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE A 189 TYR 0.019 0.001 TYR E 94 ARG 0.002 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.429 Fit side-chains REVERT: R 260 ARG cc_start: 0.7301 (tpt90) cc_final: 0.6591 (tpp80) REVERT: A 33 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: A 255 ASN cc_start: 0.8552 (m-40) cc_final: 0.8245 (m-40) REVERT: B 197 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6253 (mpt90) REVERT: C 21 MET cc_start: 0.5418 (ttm) cc_final: 0.4689 (tpp) REVERT: E 187 GLN cc_start: 0.7522 (pt0) cc_final: 0.7147 (pt0) REVERT: M 67 MET cc_start: 0.5973 (tmm) cc_final: 0.5671 (tpp) REVERT: M 206 PHE cc_start: 0.7715 (m-80) cc_final: 0.7489 (m-80) REVERT: M 245 MET cc_start: 0.7446 (mmp) cc_final: 0.7002 (mmt) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 0.2442 time to fit residues: 63.5384 Evaluate side-chains 170 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL Chi-restraints excluded: chain M residue 313 THR Chi-restraints excluded: chain M residue 332 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 0.0870 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11970 Z= 0.367 Angle : 0.615 8.856 16303 Z= 0.316 Chirality : 0.043 0.151 1910 Planarity : 0.005 0.053 1958 Dihedral : 5.897 58.087 2305 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.94 % Allowed : 11.37 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.43 (0.22), residues: 1421 helix: 2.41 (0.19), residues: 658 sheet: 0.14 (0.29), residues: 292 loop : -0.61 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.002 HIS M 321 PHE 0.026 0.002 PHE A 189 TYR 0.033 0.002 TYR E 94 ARG 0.004 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.304 Fit side-chains REVERT: A 33 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: A 255 ASN cc_start: 0.8742 (m-40) cc_final: 0.8259 (m110) REVERT: B 52 ARG cc_start: 0.7312 (mtt-85) cc_final: 0.6854 (mtt90) REVERT: B 197 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6538 (mpt90) REVERT: B 283 ARG cc_start: 0.6893 (mmm-85) cc_final: 0.6654 (mmm-85) REVERT: C 21 MET cc_start: 0.5423 (ttm) cc_final: 0.4678 (tpp) REVERT: E 63 THR cc_start: 0.7498 (p) cc_final: 0.7205 (p) REVERT: E 187 GLN cc_start: 0.7585 (pt0) cc_final: 0.7157 (pt0) REVERT: M 67 MET cc_start: 0.6132 (tmm) cc_final: 0.5825 (tpp) REVERT: M 245 MET cc_start: 0.7416 (mmp) cc_final: 0.7020 (mmp) outliers start: 37 outliers final: 29 residues processed: 183 average time/residue: 0.2502 time to fit residues: 65.7607 Evaluate side-chains 181 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 200 ILE Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL 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: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 106 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11970 Z= 0.172 Angle : 0.483 6.317 16303 Z= 0.252 Chirality : 0.039 0.136 1910 Planarity : 0.004 0.048 1958 Dihedral : 5.305 59.736 2305 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.23 % Allowed : 12.64 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.72 (0.22), residues: 1421 helix: 2.77 (0.19), residues: 660 sheet: 0.13 (0.29), residues: 288 loop : -0.57 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.018 0.001 PHE A 189 TYR 0.019 0.001 TYR E 94 ARG 0.004 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.356 Fit side-chains REVERT: A 29 LYS cc_start: 0.7940 (mttt) cc_final: 0.7540 (mttt) REVERT: A 33 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: A 255 ASN cc_start: 0.8744 (m-40) cc_final: 0.8251 (m110) REVERT: B 52 ARG cc_start: 0.7162 (mtt-85) cc_final: 0.6722 (mtt90) REVERT: B 197 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6260 (mpt90) REVERT: C 21 MET cc_start: 0.5475 (ttm) cc_final: 0.4715 (tpp) REVERT: E 187 GLN cc_start: 0.7566 (pt0) cc_final: 0.7143 (pt0) REVERT: M 67 MET cc_start: 0.6031 (tmm) cc_final: 0.5783 (tpp) REVERT: M 72 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7215 (p) outliers start: 28 outliers final: 19 residues processed: 176 average time/residue: 0.2261 time to fit residues: 57.8217 Evaluate side-chains 173 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 219 CYS Chi-restraints excluded: chain M residue 308 VAL 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: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11970 Z= 0.152 Angle : 0.468 6.914 16303 Z= 0.244 Chirality : 0.038 0.138 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.155 59.991 2305 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.91 % Allowed : 13.51 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.91 (0.22), residues: 1421 helix: 2.96 (0.19), residues: 660 sheet: 0.25 (0.29), residues: 286 loop : -0.56 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.016 0.001 PHE A 189 TYR 0.018 0.001 TYR E 94 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.517 Fit side-chains REVERT: A 18 MET cc_start: 0.7929 (mtp) cc_final: 0.7702 (mtp) REVERT: A 29 LYS cc_start: 0.7900 (mttt) cc_final: 0.7486 (mttt) REVERT: A 33 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6626 (mm-30) REVERT: A 255 ASN cc_start: 0.8745 (m-40) cc_final: 0.8443 (m-40) REVERT: B 52 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6759 (mtt90) REVERT: B 197 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6178 (mpt90) REVERT: C 21 MET cc_start: 0.5484 (ttm) cc_final: 0.4720 (tpp) REVERT: E 187 GLN cc_start: 0.7501 (pt0) cc_final: 0.7081 (pt0) REVERT: M 67 MET cc_start: 0.6024 (tmm) cc_final: 0.5770 (tpp) REVERT: M 82 VAL cc_start: 0.7703 (p) cc_final: 0.7431 (t) outliers start: 24 outliers final: 17 residues processed: 172 average time/residue: 0.2323 time to fit residues: 57.9554 Evaluate side-chains 170 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL 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: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 259 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11970 Z= 0.184 Angle : 0.487 7.861 16303 Z= 0.252 Chirality : 0.039 0.138 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.189 59.455 2305 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.07 % Allowed : 13.43 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.93 (0.22), residues: 1421 helix: 2.95 (0.19), residues: 660 sheet: 0.29 (0.29), residues: 291 loop : -0.53 (0.28), residues: 470 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 0.017 0.001 PHE A 189 TYR 0.018 0.001 TYR E 94 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.381 Fit side-chains REVERT: A 18 MET cc_start: 0.7931 (mtp) cc_final: 0.7697 (mtp) REVERT: A 29 LYS cc_start: 0.7957 (mttt) cc_final: 0.7550 (mttt) REVERT: A 33 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: A 255 ASN cc_start: 0.8735 (m-40) cc_final: 0.8420 (m-40) REVERT: B 52 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6854 (mtt90) REVERT: B 197 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6092 (mpt90) REVERT: C 21 MET cc_start: 0.5507 (ttm) cc_final: 0.4731 (tpp) REVERT: E 187 GLN cc_start: 0.7514 (pt0) cc_final: 0.7073 (pt0) REVERT: M 67 MET cc_start: 0.6042 (tmm) cc_final: 0.5789 (tpp) REVERT: M 82 VAL cc_start: 0.7713 (p) cc_final: 0.7441 (t) outliers start: 26 outliers final: 20 residues processed: 170 average time/residue: 0.2526 time to fit residues: 61.4624 Evaluate side-chains 173 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL 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: 140 random chunks: chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.0010 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11970 Z= 0.231 Angle : 0.515 7.676 16303 Z= 0.266 Chirality : 0.040 0.140 1910 Planarity : 0.004 0.047 1958 Dihedral : 5.357 59.604 2305 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 13.28 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.82 (0.22), residues: 1421 helix: 2.85 (0.19), residues: 660 sheet: 0.24 (0.29), residues: 291 loop : -0.59 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 PHE 0.018 0.001 PHE A 189 TYR 0.022 0.001 TYR E 94 ARG 0.003 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.564 Fit side-chains REVERT: A 18 MET cc_start: 0.7899 (mtp) cc_final: 0.7663 (mtp) REVERT: A 33 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: A 255 ASN cc_start: 0.8737 (m-40) cc_final: 0.8238 (m110) REVERT: B 52 ARG cc_start: 0.7213 (mtt-85) cc_final: 0.6773 (mtt90) REVERT: B 197 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6172 (mpt90) REVERT: C 21 MET cc_start: 0.5539 (ttm) cc_final: 0.4742 (tpp) REVERT: E 187 GLN cc_start: 0.7552 (pt0) cc_final: 0.7251 (pt0) REVERT: M 67 MET cc_start: 0.6133 (tmm) cc_final: 0.5909 (tpp) REVERT: M 82 VAL cc_start: 0.7673 (p) cc_final: 0.7384 (t) REVERT: M 217 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7401 (mt) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.2294 time to fit residues: 57.1781 Evaluate side-chains 176 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 217 ILE Chi-restraints excluded: chain M residue 308 VAL 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: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.166414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126314 restraints weight = 12360.570| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.20 r_work: 0.2984 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11970 Z= 0.192 Angle : 0.488 7.165 16303 Z= 0.254 Chirality : 0.039 0.137 1910 Planarity : 0.004 0.046 1958 Dihedral : 5.255 59.879 2305 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.38 % Allowed : 13.20 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.85 (0.22), residues: 1421 helix: 2.89 (0.19), residues: 660 sheet: 0.24 (0.29), residues: 291 loop : -0.58 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS M 321 PHE 0.016 0.001 PHE A 189 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.31 seconds wall clock time: 46 minutes 14.82 seconds (2774.82 seconds total)