Starting phenix.real_space_refine on Mon Dec 30 18:05:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_33765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_33765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_33765.map" model { file = "/net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_33765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ye6_33765/12_2024/7ye6_33765.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: 8.17, per 1000 atoms: 0.59 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.47 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: 4.43 Time building geometry restraints manager: 3.79 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- 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 14105 Z= 0.190 Angle : 0.677 18.161 19160 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 : 5.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP B 279 HIS 0.002 0.000 HIS A 533 PHE 0.013 0.001 PHE B 104 TYR 0.014 0.001 TYR E 28 ARG 0.002 0.000 ARG A 49 *********************** 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 : 1.421 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: 0.3454 time to fit residues: 122.3492 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 : 1.471 ------------------------------------------------------------------------------- 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 147 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 50.0000 chunk 70 optimal weight: 0.4980 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 A 371 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 561 GLN B 40 ASN B 175 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 224 GLN E 34 GLN E 83 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14105 Z= 0.209 Angle : 0.593 14.894 19160 Z= 0.309 Chirality : 0.044 0.167 2085 Planarity : 0.004 0.068 2518 Dihedral : 4.046 46.811 1952 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.21 % Allowed : 14.49 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.17), residues: 1765 helix: -4.31 (0.20), residues: 189 sheet: -2.41 (0.21), residues: 495 loop : -2.99 (0.16), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 228 HIS 0.006 0.001 HIS B 121 PHE 0.016 0.001 PHE P1214 TYR 0.030 0.001 TYR A 477 ARG 0.006 0.001 ARG D 112 *********************** 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 202 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.5786 (m-30) cc_final: 0.5075 (m-30) REVERT: A 519 ILE cc_start: 0.8348 (tp) cc_final: 0.7888 (tp) REVERT: A 630 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 82 LYS cc_start: 0.3939 (mtmm) cc_final: 0.3406 (mtmt) REVERT: B 221 MET cc_start: 0.7025 (ptm) cc_final: 0.6693 (ptp) REVERT: B 306 MET cc_start: 0.2589 (pmm) cc_final: 0.2244 (pmm) REVERT: E 28 TYR cc_start: 0.6335 (p90) cc_final: 0.4917 (t80) REVERT: E 31 ASP cc_start: 0.7191 (p0) cc_final: 0.6898 (p0) REVERT: E 101 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6739 (pt) outliers start: 32 outliers final: 18 residues processed: 190 average time/residue: 0.2844 time to fit residues: 77.6638 Evaluate side-chains 169 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 512 ASP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 VAL 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 E residue 101 LEU Chi-restraints excluded: chain P residue 1065 VAL 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 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 88 optimal weight: 50.0000 chunk 49 optimal weight: 0.1980 chunk 132 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.0270 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN E 34 GLN P1170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14105 Z= 0.161 Angle : 0.542 13.822 19160 Z= 0.280 Chirality : 0.042 0.157 2085 Planarity : 0.003 0.047 2518 Dihedral : 3.785 24.499 1949 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.55 % Allowed : 15.53 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.17), residues: 1765 helix: -3.55 (0.25), residues: 197 sheet: -2.16 (0.22), residues: 503 loop : -2.73 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.006 0.001 HIS A 677 PHE 0.021 0.001 PHE P1018 TYR 0.019 0.001 TYR A 477 ARG 0.009 0.000 ARG D 223 *********************** 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 200 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.5860 (m-30) cc_final: 0.5322 (m-30) REVERT: A 519 ILE cc_start: 0.8377 (tp) cc_final: 0.7890 (tp) REVERT: A 630 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6790 (mp) REVERT: B 221 MET cc_start: 0.6932 (ptm) cc_final: 0.6644 (ptp) REVERT: E 28 TYR cc_start: 0.6442 (p90) cc_final: 0.4849 (t80) REVERT: E 31 ASP cc_start: 0.7258 (p0) cc_final: 0.6948 (p0) REVERT: P 1018 PHE cc_start: 0.7887 (t80) cc_final: 0.7653 (t80) outliers start: 37 outliers final: 22 residues processed: 186 average time/residue: 0.2797 time to fit residues: 75.6025 Evaluate side-chains 167 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 470 GLU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 195 VAL 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 1122 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 678 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 34 GLN P1127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14105 Z= 0.213 Angle : 0.573 13.633 19160 Z= 0.298 Chirality : 0.043 0.207 2085 Planarity : 0.004 0.039 2518 Dihedral : 4.001 29.639 1949 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.90 % Allowed : 17.12 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.18), residues: 1765 helix: -3.05 (0.29), residues: 200 sheet: -1.97 (0.22), residues: 491 loop : -2.53 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.006 0.001 HIS A 677 PHE 0.015 0.001 PHE P1274 TYR 0.022 0.001 TYR A 794 ARG 0.007 0.001 ARG P1205 *********************** 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 196 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.6907 (m-30) cc_final: 0.5282 (t70) REVERT: A 630 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7015 (mp) REVERT: B 221 MET cc_start: 0.6919 (ptm) cc_final: 0.6657 (ptp) REVERT: E 31 ASP cc_start: 0.7242 (p0) cc_final: 0.6970 (p0) REVERT: P 1018 PHE cc_start: 0.8031 (t80) cc_final: 0.7800 (t80) outliers start: 42 outliers final: 31 residues processed: 182 average time/residue: 0.2759 time to fit residues: 73.8467 Evaluate side-chains 169 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL 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 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 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS 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 140 optimal weight: 3.9990 chunk 96 optimal weight: 50.0000 chunk 2 optimal weight: 0.0770 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14105 Z= 0.200 Angle : 0.565 13.945 19160 Z= 0.295 Chirality : 0.044 0.228 2085 Planarity : 0.004 0.039 2518 Dihedral : 4.017 29.556 1949 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.45 % Allowed : 18.15 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.18), residues: 1765 helix: -2.73 (0.29), residues: 215 sheet: -1.85 (0.23), residues: 481 loop : -2.47 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.012 0.001 HIS B 324 PHE 0.015 0.001 PHE A 140 TYR 0.021 0.001 TYR A 794 ARG 0.006 0.000 ARG P1205 *********************** 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 194 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 221 MET cc_start: 0.6933 (ptm) cc_final: 0.6681 (ptp) REVERT: E 31 ASP cc_start: 0.7369 (p0) cc_final: 0.7057 (p0) REVERT: P 1018 PHE cc_start: 0.8059 (t80) cc_final: 0.7844 (t80) outliers start: 50 outliers final: 35 residues processed: 182 average time/residue: 0.2709 time to fit residues: 72.8823 Evaluate side-chains 174 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 248 THR 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 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE 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 B residue 30 VAL Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1089 SER 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 1208 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 88 optimal weight: 40.0000 chunk 163 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 340 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS A 579 ASN A 625 HIS A 765 ASN B 230 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14105 Z= 0.354 Angle : 0.694 13.553 19160 Z= 0.367 Chirality : 0.046 0.238 2085 Planarity : 0.005 0.081 2518 Dihedral : 4.728 35.818 1949 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 4.14 % Allowed : 18.22 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.18), residues: 1765 helix: -2.59 (0.31), residues: 214 sheet: -1.74 (0.23), residues: 478 loop : -2.50 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 73 HIS 0.008 0.001 HIS A 677 PHE 0.027 0.002 PHE A 494 TYR 0.033 0.002 TYR A 794 ARG 0.008 0.001 ARG P1205 *********************** 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 214 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: A 504 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8406 (p90) REVERT: A 521 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6630 (mm-30) REVERT: B 221 MET cc_start: 0.6894 (ptm) cc_final: 0.6673 (ptp) REVERT: D 178 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7148 (mp0) REVERT: E 28 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.4673 (t80) REVERT: E 31 ASP cc_start: 0.7373 (p0) cc_final: 0.7064 (p0) REVERT: E 63 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6616 (mt) REVERT: P 1018 PHE cc_start: 0.8336 (t80) cc_final: 0.7962 (t80) outliers start: 60 outliers final: 39 residues processed: 197 average time/residue: 0.3232 time to fit residues: 92.9073 Evaluate side-chains 184 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 470 GLU 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 702 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 195 VAL 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 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 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE 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 1203 ILE Chi-restraints excluded: chain P residue 1208 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 168 optimal weight: 0.9990 chunk 105 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 64 HIS B 130 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** 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** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1127 HIS ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 14105 Z= 0.413 Angle : 0.724 13.007 19160 Z= 0.387 Chirality : 0.048 0.243 2085 Planarity : 0.005 0.092 2518 Dihedral : 5.016 37.018 1949 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 4.35 % Allowed : 19.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.19), residues: 1765 helix: -2.53 (0.31), residues: 202 sheet: -1.75 (0.24), residues: 477 loop : -2.40 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 206 HIS 0.008 0.002 HIS A 677 PHE 0.028 0.002 PHE A 494 TYR 0.041 0.002 TYR P1286 ARG 0.009 0.001 ARG P1205 *********************** 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 211 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7592 (m-10) REVERT: B 221 MET cc_start: 0.6776 (ptm) cc_final: 0.6570 (ptp) REVERT: D 178 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7174 (mp0) REVERT: E 28 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.4290 (t80) REVERT: E 31 ASP cc_start: 0.7469 (p0) cc_final: 0.7221 (p0) outliers start: 63 outliers final: 51 residues processed: 193 average time/residue: 0.2766 time to fit residues: 78.6626 Evaluate side-chains 192 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE 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 633 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 743 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 195 VAL 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 P residue 1080 THR Chi-restraints excluded: chain P residue 1084 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1089 SER 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 1208 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 83 optimal weight: 40.0000 chunk 15 optimal weight: 40.0000 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 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** D 226 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14105 Z= 0.291 Angle : 0.668 14.686 19160 Z= 0.352 Chirality : 0.046 0.314 2085 Planarity : 0.005 0.064 2518 Dihedral : 4.737 35.255 1949 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.80 % Allowed : 20.63 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.19), residues: 1765 helix: -2.31 (0.32), residues: 202 sheet: -1.73 (0.24), residues: 474 loop : -2.32 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.005 0.001 HIS A 677 PHE 0.034 0.002 PHE P1018 TYR 0.039 0.002 TYR P1144 ARG 0.006 0.001 ARG P1205 *********************** 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 202 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: A 504 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8419 (p90) REVERT: D 124 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5975 (mt) REVERT: E 28 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.4614 (t80) outliers start: 55 outliers final: 46 residues processed: 186 average time/residue: 0.2520 time to fit residues: 69.0721 Evaluate side-chains 189 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU 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 545 MET 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 633 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 743 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 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 P residue 1085 THR Chi-restraints excluded: chain P residue 1089 SER 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 1208 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 20.0000 chunk 147 optimal weight: 0.0570 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 0.0770 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14105 Z= 0.163 Angle : 0.613 14.951 19160 Z= 0.316 Chirality : 0.044 0.247 2085 Planarity : 0.004 0.054 2518 Dihedral : 4.263 28.548 1949 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.28 % Allowed : 22.71 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.19), residues: 1765 helix: -1.88 (0.35), residues: 181 sheet: -1.59 (0.23), residues: 481 loop : -2.15 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.006 0.001 HIS A 677 PHE 0.019 0.001 PHE P1018 TYR 0.026 0.001 TYR A 468 ARG 0.004 0.000 ARG D 223 *********************** 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 184 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 ILE cc_start: 0.7935 (pt) cc_final: 0.7379 (mm) REVERT: A 791 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5483 (t80) REVERT: E 28 TYR cc_start: 0.7981 (p90) cc_final: 0.4672 (t80) REVERT: P 1058 ASP cc_start: 0.7348 (p0) cc_final: 0.7125 (p0) outliers start: 33 outliers final: 29 residues processed: 169 average time/residue: 0.2772 time to fit residues: 68.8881 Evaluate side-chains 176 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 481 ASP Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain P residue 1089 SER 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 1172 GLU Chi-restraints excluded: chain P residue 1209 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 174 optimal weight: 0.4980 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 110 optimal weight: 0.0980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 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 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14105 Z= 0.378 Angle : 0.747 14.300 19160 Z= 0.391 Chirality : 0.048 0.303 2085 Planarity : 0.005 0.079 2518 Dihedral : 4.816 35.783 1949 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.17 % Allowed : 22.29 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.19), residues: 1765 helix: -2.09 (0.33), residues: 203 sheet: -1.65 (0.24), residues: 475 loop : -2.25 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 745 HIS 0.006 0.001 HIS A 555 PHE 0.029 0.002 PHE A 494 TYR 0.031 0.002 TYR A 477 ARG 0.008 0.001 ARG P1142 ********************** 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 190 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.1803 (OUTLIER) cc_final: 0.1389 (m) REVERT: A 428 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: A 504 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8412 (p90) REVERT: A 791 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5412 (t80) REVERT: C 56 MET cc_start: 0.5235 (pmm) cc_final: 0.5017 (pmm) REVERT: D 124 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5854 (mt) REVERT: D 178 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7117 (mp0) REVERT: E 28 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.4362 (t80) REVERT: P 1170 GLN cc_start: 0.7334 (mt0) cc_final: 0.6921 (pt0) outliers start: 46 outliers final: 32 residues processed: 174 average time/residue: 0.2617 time to fit residues: 67.8698 Evaluate side-chains 174 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 428 PHE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 82 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 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 61 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 1261 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 128 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 0.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 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 72 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.283957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.225996 restraints weight = 16965.621| |-----------------------------------------------------------------------------| r_work (start): 0.4810 rms_B_bonded: 3.48 r_work: 0.4459 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14105 Z= 0.208 Angle : 0.670 14.875 19160 Z= 0.345 Chirality : 0.045 0.270 2085 Planarity : 0.004 0.071 2518 Dihedral : 4.499 33.161 1949 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.48 % Allowed : 23.33 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.19), residues: 1765 helix: -2.01 (0.33), residues: 203 sheet: -1.60 (0.24), residues: 485 loop : -2.14 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS P1062 PHE 0.020 0.001 PHE P1018 TYR 0.026 0.001 TYR A 477 ARG 0.008 0.001 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.01 seconds wall clock time: 52 minutes 24.71 seconds (3144.71 seconds total)