Starting phenix.real_space_refine on Wed Feb 4 22:47:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye6_33765/02_2026/7ye6_33765.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 40 5.16 5 C 8707 2.51 5 N 2351 2.21 5 O 2706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13804 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6205 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2695 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 353} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 390 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 671 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "P" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2121 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13804 At special positions: 0 Unit cell: (135.876, 120.666, 145.002, 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 40 16.00 O 2706 8.00 N 2351 7.00 C 8707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS P1297 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.07 Conformation dependent library (CDL) restraints added in 629.7 milliseconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 18 sheets defined 12.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 removed outlier: 4.058A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.602A pdb=" N LEU A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.070A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.631A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 223' Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.574A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.892A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 303' Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.573A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.614A pdb=" N ARG A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.805A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.665A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.993A pdb=" N TYR D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.434A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.883A pdb=" N ALA D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 79' Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.703A pdb=" N ALA D 90 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE D 92 " --> pdb=" O GLN D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 93 through 98 removed outlier: 4.434A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.626A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 4.338A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 removed outlier: 4.051A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.727A pdb=" N TYR D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.657A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.139A pdb=" N ASP D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.845A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.580A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 1012 through 1020 removed outlier: 4.132A pdb=" N LYS P1016 " --> pdb=" O SER P1012 " (cutoff:3.500A) Processing helix chain 'P' and resid 1024 through 1029 removed outlier: 3.682A pdb=" N ARG P1028 " --> pdb=" O ASN P1024 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET P1029 " --> pdb=" O LEU P1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1024 through 1029' Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.241A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET A 325 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.622A pdb=" N ARG A 353 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 416 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 removed outlier: 3.512A pdb=" N SER A 484 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 529 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 525 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.836A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 745 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.610A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 387 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 390 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 374 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 379 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.029A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 95 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.117A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.655A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.775A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.804A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS B 347 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.546A pdb=" N GLN E 79 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 90 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.991A pdb=" N ASP E 66 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR E 72 " --> pdb=" O ASP E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'P' and resid 1042 through 1043 removed outlier: 4.731A pdb=" N TRP P1042 " --> pdb=" O GLY P1066 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P1066 " --> pdb=" O TRP P1042 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P1088 " --> pdb=" O THR P1061 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS P1101 " --> pdb=" O ASP P1129 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP P1129 " --> pdb=" O LYS P1101 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR P1175 " --> pdb=" O ALA P1151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY P1204 " --> pdb=" O PHE P1231 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P1208 " --> pdb=" O LEU P1227 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY P1228 " --> pdb=" O LEU P1259 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG P1257 " --> pdb=" O GLN P1230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 1042 through 1043 removed outlier: 4.731A pdb=" N TRP P1042 " --> pdb=" O GLY P1066 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P1066 " --> pdb=" O TRP P1042 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR P1049 " --> pdb=" O ASP P1289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 1213 through 1215 removed outlier: 3.586A pdb=" N LYS P1220 " --> pdb=" O GLU P1267 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4604 1.34 - 1.46: 3338 1.46 - 1.58: 6086 1.58 - 1.70: 1 1.70 - 1.82: 76 Bond restraints: 14105 Sorted by residual: bond pdb=" C PRO A 721 " pdb=" N THR A 722 " ideal model delta sigma weight residual 1.331 1.369 -0.038 2.07e-02 2.33e+03 3.43e+00 bond pdb=" CA THR B 315 " pdb=" CB THR B 315 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" N GLN A 87 " pdb=" CA GLN A 87 " ideal model delta sigma weight residual 1.460 1.479 -0.019 1.45e-02 4.76e+03 1.79e+00 bond pdb=" CB ARG B 273 " pdb=" CG ARG B 273 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CA LEU A 365 " pdb=" CB LEU A 365 " ideal model delta sigma weight residual 1.539 1.604 -0.064 4.88e-02 4.20e+02 1.73e+00 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 19067 3.63 - 7.26: 83 7.26 - 10.90: 9 10.90 - 14.53: 0 14.53 - 18.16: 1 Bond angle restraints: 19160 Sorted by residual: angle pdb=" CA LEU E 101 " pdb=" CB LEU E 101 " pdb=" CG LEU E 101 " ideal model delta sigma weight residual 116.30 134.46 -18.16 3.50e+00 8.16e-02 2.69e+01 angle pdb=" C VAL B 254 " pdb=" N ASN B 255 " pdb=" CA ASN B 255 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C VAL B 314 " pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" CA TYR A 504 " pdb=" CB TYR A 504 " pdb=" CG TYR A 504 " ideal model delta sigma weight residual 113.90 121.23 -7.33 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C GLY C 55 " pdb=" N MET C 56 " pdb=" CA MET C 56 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 ... (remaining 19155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 7486 17.30 - 34.61: 639 34.61 - 51.91: 123 51.91 - 69.22: 17 69.22 - 86.52: 12 Dihedral angle restraints: 8277 sinusoidal: 3175 harmonic: 5102 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA CYS P1297 " pdb=" C CYS P1297 " pdb=" N TYR P1298 " pdb=" CA TYR P1298 " ideal model delta harmonic sigma weight residual 180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CB CYS A 427 " pdb=" SG CYS A 427 " pdb=" SG CYS P1297 " pdb=" CB CYS P1297 " ideal model delta sinusoidal sigma weight residual 93.00 41.88 51.12 1 1.00e+01 1.00e-02 3.57e+01 ... (remaining 8274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1740 0.062 - 0.124: 308 0.124 - 0.187: 32 0.187 - 0.249: 4 0.249 - 0.311: 1 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CB VAL D 234 " pdb=" CA VAL D 234 " pdb=" CG1 VAL D 234 " pdb=" CG2 VAL D 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA CYS A 427 " pdb=" N CYS A 427 " pdb=" C CYS A 427 " pdb=" CB CYS A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA CYS P1297 " pdb=" N CYS P1297 " pdb=" C CYS P1297 " pdb=" CB CYS P1297 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2082 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 215 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO D 216 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 722 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 723 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 723 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 723 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 67 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 68 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.027 5.00e-02 4.00e+02 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2894 2.78 - 3.31: 11119 3.31 - 3.84: 22503 3.84 - 4.37: 24433 4.37 - 4.90: 43008 Nonbonded interactions: 103957 Sorted by model distance: nonbonded pdb=" OG SER B 285 " pdb=" O VAL B 299 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 761 " pdb=" OG SER A 761 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 715 " pdb=" OD1 ASP A 740 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.333 3.040 nonbonded pdb=" OG SER A 274 " pdb=" O VAL A 339 " model vdw 2.345 3.040 ... (remaining 103952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.780 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 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 : 0.003 0.064 14107 Z= 0.144 Angle : 0.678 18.161 19164 Z= 0.365 Chirality : 0.048 0.311 2085 Planarity : 0.004 0.055 2518 Dihedral : 13.340 86.522 5035 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.28 % Allowed : 7.52 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.15), residues: 1765 helix: -5.24 (0.09), residues: 184 sheet: -2.71 (0.21), residues: 484 loop : -3.36 (0.14), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.014 0.001 TYR E 28 PHE 0.013 0.001 PHE B 104 TRP 0.005 0.001 TRP B 279 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00283 (14105) covalent geometry : angle 0.67669 (19160) SS BOND : bond 0.00989 ( 2) SS BOND : angle 2.95304 ( 4) hydrogen bonds : bond 0.31226 ( 296) hydrogen bonds : angle 11.37008 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (pp) REVERT: A 387 GLU cc_start: 0.6840 (pt0) cc_final: 0.6610 (tm-30) REVERT: A 390 ASN cc_start: 0.8125 (t0) cc_final: 0.7795 (p0) REVERT: A 399 ASP cc_start: 0.6410 (m-30) cc_final: 0.5816 (m-30) REVERT: A 519 ILE cc_start: 0.7940 (tp) cc_final: 0.7551 (tp) REVERT: A 601 ILE cc_start: 0.7569 (pt) cc_final: 0.6876 (mm) REVERT: A 736 SER cc_start: 0.8183 (m) cc_final: 0.7843 (t) REVERT: B 306 MET cc_start: 0.3219 (pmm) cc_final: 0.1564 (pmm) REVERT: E 28 TYR cc_start: 0.5201 (p90) cc_final: 0.4630 (t80) REVERT: E 31 ASP cc_start: 0.7053 (p0) cc_final: 0.6581 (p0) REVERT: P 1154 GLU cc_start: 0.6945 (tp30) cc_final: 0.6687 (tp30) REVERT: P 1170 GLN cc_start: 0.6916 (mt0) cc_final: 0.6493 (tt0) outliers start: 4 outliers final: 2 residues processed: 255 average time/residue: 0.1335 time to fit residues: 47.1579 Evaluate side-chains 167 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 185 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 459 ASN A 533 HIS A 538 ASN A 561 GLN A 579 ASN A 678 GLN B 40 ASN B 175 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN D 41 GLN D 70 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 224 GLN D 226 GLN E 34 GLN E 83 HIS P1127 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.285300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.237839 restraints weight = 16408.150| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 3.11 r_work: 0.4544 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14107 Z= 0.212 Angle : 0.662 14.291 19164 Z= 0.350 Chirality : 0.045 0.193 2085 Planarity : 0.005 0.063 2518 Dihedral : 4.432 42.723 1952 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.90 % Allowed : 14.91 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.17), residues: 1765 helix: -4.26 (0.20), residues: 197 sheet: -2.56 (0.21), residues: 501 loop : -2.94 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 273 TYR 0.032 0.002 TYR A 477 PHE 0.020 0.002 PHE A 804 TRP 0.014 0.001 TRP A 546 HIS 0.008 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00468 (14105) covalent geometry : angle 0.65924 (19160) SS BOND : bond 0.00443 ( 2) SS BOND : angle 4.07759 ( 4) hydrogen bonds : bond 0.04680 ( 296) hydrogen bonds : angle 7.02965 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.6688 (m-30) cc_final: 0.4820 (t70) REVERT: A 727 ASP cc_start: 0.3761 (OUTLIER) cc_final: 0.3552 (p0) REVERT: B 82 LYS cc_start: 0.4266 (mtmm) cc_final: 0.3668 (mtmt) REVERT: B 221 MET cc_start: 0.7251 (ptm) cc_final: 0.7006 (ptp) REVERT: B 306 MET cc_start: 0.3096 (pmm) cc_final: 0.2586 (pmm) REVERT: E 31 ASP cc_start: 0.7438 (p0) cc_final: 0.7161 (p0) REVERT: E 101 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7033 (pt) REVERT: P 1150 TYR cc_start: 0.7577 (m-80) cc_final: 0.7319 (m-80) outliers start: 42 outliers final: 25 residues processed: 197 average time/residue: 0.1237 time to fit residues: 35.1228 Evaluate side-chains 173 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 93 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 11 optimal weight: 40.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 579 ASN A 625 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.280688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.237954 restraints weight = 16572.598| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 2.54 r_work: 0.4388 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14107 Z= 0.241 Angle : 0.680 12.812 19164 Z= 0.361 Chirality : 0.046 0.261 2085 Planarity : 0.005 0.092 2518 Dihedral : 4.674 35.664 1949 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.66 % Allowed : 17.53 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.17), residues: 1765 helix: -3.44 (0.26), residues: 206 sheet: -2.16 (0.22), residues: 494 loop : -2.75 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 367 TYR 0.038 0.002 TYR A 794 PHE 0.026 0.002 PHE A 494 TRP 0.011 0.001 TRP E 73 HIS 0.008 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00535 (14105) covalent geometry : angle 0.67672 (19160) SS BOND : bond 0.00481 ( 2) SS BOND : angle 4.56276 ( 4) hydrogen bonds : bond 0.04822 ( 296) hydrogen bonds : angle 6.53748 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: A 504 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8334 (p90) REVERT: A 512 ASP cc_start: 0.8223 (p0) cc_final: 0.7795 (p0) REVERT: A 552 MET cc_start: 0.6078 (ptm) cc_final: 0.5686 (ppp) REVERT: A 630 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 727 ASP cc_start: 0.4438 (OUTLIER) cc_final: 0.4215 (p0) REVERT: B 82 LYS cc_start: 0.5029 (mtmm) cc_final: 0.4563 (mtmt) REVERT: B 306 MET cc_start: 0.3106 (pmm) cc_final: 0.2697 (pmm) REVERT: C 56 MET cc_start: 0.5810 (pmm) cc_final: 0.5228 (pmm) REVERT: D 109 MET cc_start: 0.6341 (tmm) cc_final: 0.5937 (tpt) REVERT: E 31 ASP cc_start: 0.7268 (p0) cc_final: 0.6968 (p0) REVERT: E 63 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7251 (mt) REVERT: P 1018 PHE cc_start: 0.8577 (t80) cc_final: 0.8090 (t80) outliers start: 53 outliers final: 36 residues processed: 201 average time/residue: 0.1134 time to fit residues: 32.9701 Evaluate side-chains 183 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 579 ASN A 765 ASN B 64 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN P1127 HIS ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.274959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.223125 restraints weight = 16429.673| |-----------------------------------------------------------------------------| r_work (start): 0.4810 rms_B_bonded: 3.09 r_work: 0.4254 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.006 0.095 14107 Z= 0.270 Angle : 0.703 13.548 19164 Z= 0.374 Chirality : 0.047 0.292 2085 Planarity : 0.005 0.101 2518 Dihedral : 4.882 35.200 1949 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 5.24 % Allowed : 18.63 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.18), residues: 1765 helix: -2.90 (0.29), residues: 200 sheet: -2.08 (0.22), residues: 505 loop : -2.63 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P1273 TYR 0.035 0.002 TYR A 794 PHE 0.028 0.002 PHE A 494 TRP 0.011 0.001 TRP A 745 HIS 0.007 0.002 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00601 (14105) covalent geometry : angle 0.69945 (19160) SS BOND : bond 0.00390 ( 2) SS BOND : angle 5.17559 ( 4) hydrogen bonds : bond 0.04466 ( 296) hydrogen bonds : angle 6.50444 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8188 (mtp) cc_final: 0.7821 (ptp) REVERT: A 512 ASP cc_start: 0.8053 (p0) cc_final: 0.7684 (p0) REVERT: B 82 LYS cc_start: 0.4918 (mtmm) cc_final: 0.4435 (mtmt) REVERT: B 306 MET cc_start: 0.3340 (pmm) cc_final: 0.3088 (pmm) REVERT: C 80 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.3844 (pt) REVERT: D 109 MET cc_start: 0.6723 (tmm) cc_final: 0.6232 (tpt) REVERT: D 174 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (pp) REVERT: E 28 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.4722 (t80) REVERT: E 31 ASP cc_start: 0.7568 (p0) cc_final: 0.7266 (p0) REVERT: E 63 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7402 (mt) REVERT: P 1018 PHE cc_start: 0.8509 (t80) cc_final: 0.8085 (t80) REVERT: P 1029 MET cc_start: 0.6213 (ptt) cc_final: 0.5978 (ptt) outliers start: 76 outliers final: 47 residues processed: 212 average time/residue: 0.1075 time to fit residues: 33.5279 Evaluate side-chains 190 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 149 optimal weight: 0.9980 chunk 92 optimal weight: 40.0000 chunk 53 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 230 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.279406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.227688 restraints weight = 16736.612| |-----------------------------------------------------------------------------| r_work (start): 0.4853 rms_B_bonded: 3.49 r_work: 0.4211 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14107 Z= 0.142 Angle : 0.603 11.935 19164 Z= 0.317 Chirality : 0.044 0.242 2085 Planarity : 0.004 0.068 2518 Dihedral : 4.432 31.900 1949 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.28 % Allowed : 20.70 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.18), residues: 1765 helix: -2.48 (0.32), residues: 199 sheet: -2.01 (0.22), residues: 506 loop : -2.53 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 223 TYR 0.022 0.001 TYR A 477 PHE 0.016 0.001 PHE A 494 TRP 0.012 0.001 TRP A 546 HIS 0.011 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00317 (14105) covalent geometry : angle 0.59883 (19160) SS BOND : bond 0.00257 ( 2) SS BOND : angle 4.84964 ( 4) hydrogen bonds : bond 0.03487 ( 296) hydrogen bonds : angle 6.04715 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8296 (mtp) cc_final: 0.7857 (ptp) REVERT: A 504 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8342 (p90) REVERT: A 552 MET cc_start: 0.5849 (ptm) cc_final: 0.5640 (ppp) REVERT: A 630 LEU cc_start: 0.7446 (tp) cc_final: 0.7245 (tp) REVERT: A 791 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.5755 (t80) REVERT: B 82 LYS cc_start: 0.5105 (mtmm) cc_final: 0.4665 (mtmt) REVERT: C 80 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.3848 (pt) REVERT: D 109 MET cc_start: 0.6708 (tmm) cc_final: 0.6388 (tpt) REVERT: D 174 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (pp) REVERT: E 28 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.4642 (t80) REVERT: E 31 ASP cc_start: 0.7528 (p0) cc_final: 0.7169 (p0) REVERT: E 63 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7244 (mt) REVERT: P 1018 PHE cc_start: 0.8524 (t80) cc_final: 0.8159 (t80) outliers start: 62 outliers final: 45 residues processed: 195 average time/residue: 0.1091 time to fit residues: 31.4082 Evaluate side-chains 190 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 93 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 172 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.279384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.236915 restraints weight = 16661.939| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 2.61 r_work: 0.4292 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14107 Z= 0.145 Angle : 0.601 11.122 19164 Z= 0.315 Chirality : 0.044 0.218 2085 Planarity : 0.004 0.060 2518 Dihedral : 4.334 31.266 1949 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.76 % Allowed : 21.67 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.18), residues: 1765 helix: -2.25 (0.33), residues: 195 sheet: -1.92 (0.22), residues: 501 loop : -2.44 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 223 TYR 0.018 0.001 TYR A 477 PHE 0.016 0.001 PHE A 494 TRP 0.012 0.001 TRP A 546 HIS 0.008 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00326 (14105) covalent geometry : angle 0.59766 (19160) SS BOND : bond 0.00268 ( 2) SS BOND : angle 4.51484 ( 4) hydrogen bonds : bond 0.03443 ( 296) hydrogen bonds : angle 5.90321 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8444 (mtp) cc_final: 0.7990 (ptp) REVERT: A 504 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8392 (p90) REVERT: A 552 MET cc_start: 0.5875 (ptm) cc_final: 0.5429 (ppp) REVERT: A 791 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6337 (t80) REVERT: B 82 LYS cc_start: 0.5393 (mtmm) cc_final: 0.5055 (mtmt) REVERT: C 80 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.3967 (pt) REVERT: D 109 MET cc_start: 0.7094 (tmm) cc_final: 0.6739 (tpt) REVERT: D 174 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8119 (pp) REVERT: E 28 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.4440 (t80) REVERT: E 31 ASP cc_start: 0.7579 (p0) cc_final: 0.7241 (p0) REVERT: E 50 MET cc_start: 0.7717 (mmm) cc_final: 0.7401 (mmm) REVERT: E 63 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7222 (mt) REVERT: P 1018 PHE cc_start: 0.8553 (t80) cc_final: 0.8176 (t80) outliers start: 69 outliers final: 51 residues processed: 202 average time/residue: 0.1197 time to fit residues: 35.3892 Evaluate side-chains 200 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.288971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.243060 restraints weight = 16927.036| |-----------------------------------------------------------------------------| r_work (start): 0.4922 rms_B_bonded: 2.81 r_work: 0.4380 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14107 Z= 0.113 Angle : 0.586 12.608 19164 Z= 0.304 Chirality : 0.044 0.281 2085 Planarity : 0.004 0.053 2518 Dihedral : 4.152 28.833 1949 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.07 % Allowed : 22.77 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.18), residues: 1765 helix: -2.03 (0.33), residues: 206 sheet: -1.84 (0.22), residues: 508 loop : -2.41 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.021 0.001 TYR P1118 PHE 0.013 0.001 PHE P1096 TRP 0.013 0.001 TRP A 546 HIS 0.008 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00257 (14105) covalent geometry : angle 0.58154 (19160) SS BOND : bond 0.00491 ( 2) SS BOND : angle 4.93723 ( 4) hydrogen bonds : bond 0.03069 ( 296) hydrogen bonds : angle 5.62662 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8247 (mtp) cc_final: 0.7875 (ptp) REVERT: A 504 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8148 (p90) REVERT: A 521 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6919 (mm-30) REVERT: A 552 MET cc_start: 0.5955 (ptm) cc_final: 0.5551 (ppp) REVERT: A 791 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6042 (t80) REVERT: B 82 LYS cc_start: 0.5226 (mtmm) cc_final: 0.4820 (mtmt) REVERT: C 80 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.3887 (pt) REVERT: D 109 MET cc_start: 0.7226 (tmm) cc_final: 0.7016 (tpt) REVERT: D 174 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8204 (pp) REVERT: E 28 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.4795 (t80) REVERT: E 31 ASP cc_start: 0.7518 (p0) cc_final: 0.7197 (p0) REVERT: E 63 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7062 (mt) REVERT: P 1018 PHE cc_start: 0.8525 (t80) cc_final: 0.8199 (t80) outliers start: 59 outliers final: 43 residues processed: 192 average time/residue: 0.1197 time to fit residues: 33.6958 Evaluate side-chains 191 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1170 GLN Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 148 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1170 GLN P1295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.284646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.234801 restraints weight = 16963.741| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 2.88 r_work: 0.4382 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14107 Z= 0.221 Angle : 0.675 12.982 19164 Z= 0.356 Chirality : 0.046 0.295 2085 Planarity : 0.004 0.060 2518 Dihedral : 4.645 35.406 1949 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 4.49 % Allowed : 22.43 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.19), residues: 1765 helix: -2.00 (0.33), residues: 205 sheet: -1.91 (0.22), residues: 507 loop : -2.30 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.026 0.002 TYR A 477 PHE 0.023 0.002 PHE A 494 TRP 0.009 0.001 TRP A 745 HIS 0.006 0.002 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00491 (14105) covalent geometry : angle 0.67127 (19160) SS BOND : bond 0.00635 ( 2) SS BOND : angle 5.20004 ( 4) hydrogen bonds : bond 0.04059 ( 296) hydrogen bonds : angle 6.00547 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8443 (p90) REVERT: A 512 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7761 (p0) REVERT: A 791 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.5694 (t80) REVERT: B 82 LYS cc_start: 0.4650 (mtmm) cc_final: 0.4260 (mtmt) REVERT: C 80 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.3953 (pt) REVERT: D 174 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8124 (pp) REVERT: E 28 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.4290 (t80) REVERT: E 31 ASP cc_start: 0.7700 (p0) cc_final: 0.7489 (p0) REVERT: E 50 MET cc_start: 0.7433 (mmm) cc_final: 0.6937 (mmm) REVERT: P 1018 PHE cc_start: 0.8514 (t80) cc_final: 0.8109 (t80) outliers start: 65 outliers final: 51 residues processed: 190 average time/residue: 0.1072 time to fit residues: 29.4622 Evaluate side-chains 195 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1112 MET Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1170 GLN Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 93 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 131 optimal weight: 9.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.290118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.239432 restraints weight = 17756.475| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 3.41 r_work: 0.4173 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14107 Z= 0.106 Angle : 0.605 10.491 19164 Z= 0.311 Chirality : 0.044 0.247 2085 Planarity : 0.004 0.055 2518 Dihedral : 4.219 27.875 1949 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.31 % Allowed : 24.02 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.19), residues: 1765 helix: -1.72 (0.35), residues: 201 sheet: -1.78 (0.22), residues: 506 loop : -2.28 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.022 0.001 TYR P1118 PHE 0.016 0.001 PHE P1096 TRP 0.014 0.001 TRP A 546 HIS 0.005 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00242 (14105) covalent geometry : angle 0.60164 (19160) SS BOND : bond 0.00273 ( 2) SS BOND : angle 4.71595 ( 4) hydrogen bonds : bond 0.03073 ( 296) hydrogen bonds : angle 5.59376 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8707 (mtt) cc_final: 0.8123 (mtp) REVERT: A 504 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8171 (p90) REVERT: A 521 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7291 (tp30) REVERT: A 791 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 82 LYS cc_start: 0.5694 (mtmm) cc_final: 0.5410 (mtmt) REVERT: C 80 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4164 (pt) REVERT: D 174 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8094 (pp) REVERT: E 28 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.4468 (t80) REVERT: E 31 ASP cc_start: 0.7685 (p0) cc_final: 0.7432 (p0) REVERT: E 50 MET cc_start: 0.7888 (mmm) cc_final: 0.7010 (mmm) REVERT: P 1018 PHE cc_start: 0.8574 (t80) cc_final: 0.8239 (t80) outliers start: 48 outliers final: 40 residues processed: 175 average time/residue: 0.1103 time to fit residues: 28.1406 Evaluate side-chains 183 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 86 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 42 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.286975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.236962 restraints weight = 17484.044| |-----------------------------------------------------------------------------| r_work (start): 0.4859 rms_B_bonded: 2.93 r_work: 0.4359 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14107 Z= 0.175 Angle : 0.647 10.755 19164 Z= 0.335 Chirality : 0.045 0.280 2085 Planarity : 0.004 0.057 2518 Dihedral : 4.426 32.431 1949 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.38 % Allowed : 23.60 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.19), residues: 1765 helix: -1.73 (0.35), residues: 207 sheet: -1.74 (0.22), residues: 508 loop : -2.24 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P1142 TYR 0.020 0.002 TYR A 477 PHE 0.019 0.001 PHE A 494 TRP 0.011 0.001 TRP A 546 HIS 0.006 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00394 (14105) covalent geometry : angle 0.64287 (19160) SS BOND : bond 0.00552 ( 2) SS BOND : angle 4.82016 ( 4) hydrogen bonds : bond 0.03546 ( 296) hydrogen bonds : angle 5.64763 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8575 (mtt) cc_final: 0.7972 (mtp) REVERT: A 428 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: A 504 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8341 (p90) REVERT: A 552 MET cc_start: 0.7530 (ppp) cc_final: 0.7071 (ppp) REVERT: A 791 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6122 (t80) REVERT: B 82 LYS cc_start: 0.5444 (mtmm) cc_final: 0.5098 (mtmt) REVERT: C 80 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4272 (pt) REVERT: D 174 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (pp) REVERT: E 28 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.4424 (t80) REVERT: E 50 MET cc_start: 0.7877 (mmm) cc_final: 0.7050 (mmm) REVERT: P 1018 PHE cc_start: 0.8599 (t80) cc_final: 0.8299 (t80) outliers start: 49 outliers final: 42 residues processed: 181 average time/residue: 0.1163 time to fit residues: 31.2095 Evaluate side-chains 187 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 0.0000 chunk 170 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.288052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.243564 restraints weight = 17262.310| |-----------------------------------------------------------------------------| r_work (start): 0.4926 rms_B_bonded: 2.80 r_work: 0.4244 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14107 Z= 0.108 Angle : 0.610 10.598 19164 Z= 0.311 Chirality : 0.044 0.241 2085 Planarity : 0.004 0.055 2518 Dihedral : 4.150 28.058 1949 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.17 % Allowed : 23.95 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.19), residues: 1765 helix: -1.51 (0.35), residues: 204 sheet: -1.65 (0.22), residues: 508 loop : -2.17 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 273 TYR 0.016 0.001 TYR A 477 PHE 0.015 0.001 PHE P1096 TRP 0.013 0.001 TRP A 546 HIS 0.005 0.001 HIS P1062 Details of bonding type rmsd covalent geometry : bond 0.00249 (14105) covalent geometry : angle 0.60621 (19160) SS BOND : bond 0.00290 ( 2) SS BOND : angle 4.43769 ( 4) hydrogen bonds : bond 0.02944 ( 296) hydrogen bonds : angle 5.37676 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.34 seconds wall clock time: 67 minutes 19.54 seconds (4039.54 seconds total)