Starting phenix.real_space_refine on Thu Aug 6 05:35:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic3_52828/08_2026/9ic3_52828.map" } resolution = 2.96 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= 0.164 sd= 0.917 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 44 5.49 5 S 73 5.16 5 C 8690 2.51 5 N 2413 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13841 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7313 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 62, 'TRANS': 855} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345} Chain breaks: 6 Chain: "C" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2774 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {' CA': 3, 'DCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.95, per 1000 atoms: 0.21 Number of scatterers: 13841 At special positions: 0 Unit cell: (96.876, 110.952, 142.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 73 16.00 P 44 15.00 O 2618 8.00 N 2413 7.00 C 8690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.15 Conformation dependent library (CDL) restraints added in 795.4 milliseconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 44.4% alpha, 11.2% beta 18 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.686A pdb=" N HIS A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.621A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.568A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.738A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.573A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.722A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.985A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 4.077A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.635A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 553 Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.810A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 787 through 804 removed outlier: 4.759A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.666A pdb=" N ILE A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 988 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.574A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1205 through 1211 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 74 through 94 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.595A pdb=" N HIS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.067A pdb=" N PHE B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.761A pdb=" N PHE B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 removed outlier: 3.944A pdb=" N ASN B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 441 through 457 removed outlier: 4.347A pdb=" N ARG B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 74 through 94 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.531A pdb=" N GLU C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.680A pdb=" N ASP C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 240 removed outlier: 4.059A pdb=" N PHE C 240 " --> pdb=" O TRP C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 289 removed outlier: 4.529A pdb=" N LEU C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.614A pdb=" N THR C 295 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 444 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.939A pdb=" N VAL A 185 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 177 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 5.829A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.942A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 615 removed outlier: 4.575A pdb=" N PHE A 749 " --> pdb=" O TYR A 739 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 888 removed outlier: 6.899A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1184 through 1185 Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 101 removed outlier: 3.537A pdb=" N VAL B 214 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 274 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU B 275 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 108 removed outlier: 4.068A pdb=" N GLY B 153 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 387 through 389 removed outlier: 6.791A pdb=" N VAL B 357 " --> pdb=" O TRP B 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 101 removed outlier: 5.883A pdb=" N PHE C 100 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE C 185 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 180 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 274 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE C 267 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 275 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS C 259 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AB4, first strand: chain 'C' and resid 387 through 389 removed outlier: 6.825A pdb=" N TRP C 388 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 357 " --> pdb=" O TRP C 388 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 356 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL C 415 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 358 " --> pdb=" O VAL C 415 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3778 1.33 - 1.45: 2676 1.45 - 1.57: 7607 1.57 - 1.69: 85 1.69 - 1.81: 114 Bond restraints: 14260 Sorted by residual: bond pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 1.672 1.610 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C3' DC P 15 " pdb=" C2' DC P 15 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.34e+00 bond pdb=" C3' DT P 25 " pdb=" C2' DT P 25 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.86e+00 bond pdb=" CA ASP A1126 " pdb=" C ASP A1126 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.10e-02 8.26e+03 7.73e+00 ... (remaining 14255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 19325 2.43 - 4.86: 176 4.86 - 7.28: 11 7.28 - 9.71: 0 9.71 - 12.14: 1 Bond angle restraints: 19513 Sorted by residual: angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT P 14 " pdb=" C4 DT P 14 " pdb=" O4 DT P 14 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 19508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7648 17.44 - 34.89: 520 34.89 - 52.33: 171 52.33 - 69.77: 49 69.77 - 87.22: 1 Dihedral angle restraints: 8389 sinusoidal: 3700 harmonic: 4689 Sorted by residual: dihedral pdb=" CA TYR B 264 " pdb=" C TYR B 264 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS B 51 " pdb=" C HIS B 51 " pdb=" N PHE B 52 " pdb=" CA PHE B 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ILE A 215 " pdb=" C ILE A 215 " pdb=" N SER A 216 " pdb=" CA SER A 216 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1591 0.041 - 0.083: 396 0.083 - 0.124: 141 0.124 - 0.165: 3 0.165 - 0.207: 1 Chirality restraints: 2132 Sorted by residual: chirality pdb=" C1' DCP A1304 " pdb=" C2' DCP A1304 " pdb=" N1 DCP A1304 " pdb=" O4' DCP A1304 " both_signs ideal model delta sigma weight residual False 2.25 2.46 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A1131 " pdb=" N ILE A1131 " pdb=" C ILE A1131 " pdb=" CB ILE A1131 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 2129 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 73 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 496 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C LYS A 496 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS A 496 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 497 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 588 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 589 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.020 5.00e-02 4.00e+02 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1223 2.74 - 3.28: 13518 3.28 - 3.82: 23445 3.82 - 4.36: 28339 4.36 - 4.90: 47950 Nonbonded interactions: 114475 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O GLY A 871 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 593 " pdb=" OG1 THR A 599 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP A 904 " pdb=" OG1 THR A 914 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 302 " pdb=" OH TYR A 363 " model vdw 2.209 3.040 nonbonded pdb=" ND2 ASN A 134 " pdb=" OH TYR A1166 " model vdw 2.232 3.120 ... (remaining 114470 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 42 through 54 or resid 72 through 126 or resid 145 through \ 192 or resid 204 through 328 or resid 345 through 363 or resid 366 through 395 \ or resid 398 through 457)) selection = (chain 'C' and (resid 42 through 110 or resid 116 through 169 or resid 176 throu \ gh 296 or resid 304 through 457)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.060 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 14260 Z= 0.248 Angle : 0.564 12.139 19513 Z= 0.349 Chirality : 0.040 0.207 2132 Planarity : 0.004 0.041 2347 Dihedral : 13.719 87.216 5351 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.85 % Allowed : 6.24 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.31 (0.22), residues: 1583 helix: 0.92 (0.21), residues: 643 sheet: -0.80 (0.36), residues: 216 loop : 0.02 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.010 0.001 TYR A 150 PHE 0.013 0.001 PHE A 389 TRP 0.008 0.001 TRP A1049 HIS 0.003 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.25 (14260) covalent geometry : angle 0.56373 / 0.35 (19513) hydrogen bonds : bond 0.17973 / 12.57 ( 616) hydrogen bonds : angle 7.48387 / 5.25 ( 1699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 266 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 465 ASP cc_start: 0.6842 (m-30) cc_final: 0.6530 (m-30) REVERT: A 1163 MET cc_start: 0.6545 (tpt) cc_final: 0.6312 (tpt) REVERT: A 1164 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.6768 (m-80) REVERT: A 1184 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: B 348 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 383 ASN cc_start: 0.6357 (m-40) cc_final: 0.5424 (m110) outliers start: 12 outliers final: 3 residues processed: 277 average time/residue: 0.4483 time to fit residues: 137.7504 Evaluate side-chains 167 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 398 GLN A 550 GLN A 811 GLN A1059 ASN B 87 GLN B 253 GLN B 304 ASN C 161 HIS C 374 GLN C 378 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.121704 restraints weight = 23820.839| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.58 r_work: 0.3851 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14260 Z= 0.148 Angle : 0.627 13.831 19513 Z= 0.318 Chirality : 0.042 0.192 2132 Planarity : 0.005 0.050 2347 Dihedral : 14.372 71.413 2226 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.41 % Allowed : 13.97 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.64 (0.22), residues: 1583 helix: 1.14 (0.20), residues: 654 sheet: -0.33 (0.36), residues: 225 loop : 0.16 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 546 TYR 0.021 0.002 TYR C 406 PHE 0.025 0.002 PHE A 273 TRP 0.028 0.001 TRP B 215 HIS 0.007 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (14260) covalent geometry : angle 0.62716 / 0.32 (19513) hydrogen bonds : bond 0.04641 / 3.26 ( 616) hydrogen bonds : angle 5.73161 / 4.03 ( 1699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.4185 (mt-10) REVERT: A 363 TYR cc_start: 0.7489 (m-80) cc_final: 0.7276 (m-80) REVERT: A 465 ASP cc_start: 0.7828 (m-30) cc_final: 0.7595 (m-30) REVERT: A 556 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 740 ASN cc_start: 0.7334 (m-40) cc_final: 0.7035 (p0) REVERT: A 1064 ILE cc_start: 0.6550 (tp) cc_final: 0.6342 (tp) REVERT: A 1136 GLU cc_start: 0.7453 (mp0) cc_final: 0.7062 (mp0) REVERT: A 1164 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5489 (m-80) REVERT: B 369 LEU cc_start: 0.8288 (mp) cc_final: 0.7600 (mp) REVERT: B 373 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7119 (m) REVERT: C 215 TRP cc_start: 0.6412 (t-100) cc_final: 0.6187 (t-100) REVERT: C 227 ASP cc_start: 0.7866 (p0) cc_final: 0.7614 (m-30) outliers start: 34 outliers final: 9 residues processed: 200 average time/residue: 0.3702 time to fit residues: 83.8910 Evaluate side-chains 155 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.0050 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 0.0770 chunk 68 optimal weight: 8.9990 overall best weight: 0.7354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN C 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.148207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.118498 restraints weight = 24040.918| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.85 r_work: 0.3834 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14260 Z= 0.135 Angle : 0.573 11.974 19513 Z= 0.291 Chirality : 0.040 0.154 2132 Planarity : 0.004 0.044 2347 Dihedral : 14.382 76.100 2220 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.91 % Allowed : 14.96 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.22), residues: 1583 helix: 1.32 (0.20), residues: 648 sheet: -0.31 (0.36), residues: 223 loop : 0.21 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 204 TYR 0.019 0.002 TYR C 167 PHE 0.029 0.001 PHE B 228 TRP 0.014 0.001 TRP B 215 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14260) covalent geometry : angle 0.57308 / 0.29 (19513) hydrogen bonds : bond 0.03965 / 2.78 ( 616) hydrogen bonds : angle 5.36992 / 3.79 ( 1699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: A 248 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.4176 (mt-10) REVERT: A 307 PHE cc_start: 0.5605 (t80) cc_final: 0.5253 (t80) REVERT: A 363 TYR cc_start: 0.7511 (m-80) cc_final: 0.7260 (m-80) REVERT: A 465 ASP cc_start: 0.7885 (m-30) cc_final: 0.7670 (m-30) REVERT: A 541 GLN cc_start: 0.5443 (OUTLIER) cc_final: 0.5233 (mt0) REVERT: A 556 THR cc_start: 0.8315 (p) cc_final: 0.7997 (t) REVERT: A 740 ASN cc_start: 0.7291 (m-40) cc_final: 0.7024 (p0) REVERT: A 1064 ILE cc_start: 0.6633 (tp) cc_final: 0.6401 (tp) REVERT: A 1133 ILE cc_start: 0.8384 (mp) cc_final: 0.8155 (mp) REVERT: A 1136 GLU cc_start: 0.7521 (mp0) cc_final: 0.7081 (mp0) REVERT: A 1164 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: B 373 CYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7161 (m) REVERT: C 213 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7490 (tp) REVERT: C 215 TRP cc_start: 0.6437 (t-100) cc_final: 0.6169 (t-100) REVERT: C 227 ASP cc_start: 0.7833 (p0) cc_final: 0.7532 (m-30) REVERT: C 310 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7483 (OUTLIER) outliers start: 41 outliers final: 18 residues processed: 196 average time/residue: 0.4192 time to fit residues: 92.1153 Evaluate side-chains 168 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 0.0570 chunk 128 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.146978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.116973 restraints weight = 24002.894| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.88 r_work: 0.3796 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14260 Z= 0.167 Angle : 0.583 9.649 19513 Z= 0.294 Chirality : 0.041 0.144 2132 Planarity : 0.004 0.044 2347 Dihedral : 14.360 77.928 2218 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.62 % Allowed : 15.11 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.76 (0.22), residues: 1583 helix: 1.38 (0.20), residues: 641 sheet: -0.44 (0.36), residues: 223 loop : 0.16 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1146 TYR 0.021 0.002 TYR C 167 PHE 0.020 0.002 PHE B 228 TRP 0.015 0.001 TRP A 748 HIS 0.005 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14260) covalent geometry : angle 0.58326 / 0.29 (19513) hydrogen bonds : bond 0.03834 / 2.71 ( 616) hydrogen bonds : angle 5.25582 / 3.72 ( 1699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: A 248 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4152 (mt-10) REVERT: A 556 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7967 (t) REVERT: A 740 ASN cc_start: 0.7271 (m-40) cc_final: 0.7011 (p0) REVERT: A 919 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6806 (mtt) REVERT: A 985 MET cc_start: 0.6383 (tmm) cc_final: 0.6110 (tmm) REVERT: A 1064 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6515 (tp) REVERT: A 1136 GLU cc_start: 0.7606 (mp0) cc_final: 0.7182 (mp0) REVERT: A 1153 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7592 (mt) REVERT: A 1164 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: B 373 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7137 (m) REVERT: C 213 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7493 (tp) REVERT: C 215 TRP cc_start: 0.6495 (t-100) cc_final: 0.6263 (t-100) REVERT: C 227 ASP cc_start: 0.7814 (p0) cc_final: 0.7508 (m-30) REVERT: C 254 ASP cc_start: 0.6687 (t0) cc_final: 0.6221 (t0) REVERT: C 409 MET cc_start: 0.7872 (mtp) cc_final: 0.7512 (mtp) outliers start: 51 outliers final: 21 residues processed: 185 average time/residue: 0.3872 time to fit residues: 80.7896 Evaluate side-chains 177 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 0.0270 chunk 145 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 163 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 811 GLN C 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.145690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.115136 restraints weight = 24183.446| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.93 r_work: 0.3762 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14260 Z= 0.219 Angle : 0.613 9.573 19513 Z= 0.310 Chirality : 0.043 0.144 2132 Planarity : 0.005 0.049 2347 Dihedral : 14.419 81.916 2218 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.33 % Allowed : 15.53 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.54 (0.22), residues: 1583 helix: 1.21 (0.20), residues: 647 sheet: -0.60 (0.36), residues: 223 loop : 0.03 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 233 TYR 0.022 0.002 TYR C 167 PHE 0.018 0.002 PHE A 307 TRP 0.016 0.002 TRP A 748 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (14260) covalent geometry : angle 0.61273 / 0.31 (19513) hydrogen bonds : bond 0.04008 / 2.88 ( 616) hydrogen bonds : angle 5.30910 / 3.76 ( 1699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: A 248 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.4239 (mt-10) REVERT: A 299 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6863 (mpp) REVERT: A 910 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.4582 (ptp) REVERT: A 919 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6788 (mtt) REVERT: A 985 MET cc_start: 0.6513 (tmm) cc_final: 0.6102 (tmm) REVERT: A 1064 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6586 (tp) REVERT: A 1136 GLU cc_start: 0.7728 (mp0) cc_final: 0.7285 (mp0) REVERT: A 1153 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 1163 MET cc_start: 0.6705 (tpt) cc_final: 0.5814 (tpt) REVERT: A 1164 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: B 373 CYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7161 (m) REVERT: C 205 VAL cc_start: 0.8630 (t) cc_final: 0.8370 (t) REVERT: C 213 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7581 (tp) REVERT: C 215 TRP cc_start: 0.6474 (t-100) cc_final: 0.6252 (t-100) REVERT: C 227 ASP cc_start: 0.7890 (p0) cc_final: 0.7605 (m-30) REVERT: C 409 MET cc_start: 0.7906 (mtp) cc_final: 0.7523 (mtp) outliers start: 61 outliers final: 28 residues processed: 196 average time/residue: 0.4060 time to fit residues: 90.5816 Evaluate side-chains 179 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 163 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 99 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.148088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.118189 restraints weight = 23857.834| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.83 r_work: 0.3810 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14260 Z= 0.127 Angle : 0.572 12.245 19513 Z= 0.289 Chirality : 0.040 0.163 2132 Planarity : 0.004 0.047 2347 Dihedral : 14.331 83.297 2218 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.55 % Allowed : 17.09 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.22), residues: 1583 helix: 1.46 (0.21), residues: 641 sheet: -0.55 (0.36), residues: 223 loop : 0.17 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 370 TYR 0.026 0.001 TYR C 406 PHE 0.024 0.001 PHE A 307 TRP 0.018 0.001 TRP A 748 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14260) covalent geometry : angle 0.57157 / 0.29 (19513) hydrogen bonds : bond 0.03524 / 2.50 ( 616) hydrogen bonds : angle 5.08604 / 3.59 ( 1699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: A 248 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.4097 (mt-10) REVERT: A 299 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6835 (mpp) REVERT: A 556 THR cc_start: 0.8291 (p) cc_final: 0.7972 (t) REVERT: A 740 ASN cc_start: 0.7229 (m-40) cc_final: 0.6968 (p0) REVERT: A 919 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: A 985 MET cc_start: 0.6414 (tmm) cc_final: 0.6128 (tmm) REVERT: A 1057 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.4534 (tmm) REVERT: A 1064 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6571 (tp) REVERT: A 1136 GLU cc_start: 0.7666 (mp0) cc_final: 0.7211 (mp0) REVERT: A 1153 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 1163 MET cc_start: 0.6718 (tpt) cc_final: 0.5778 (tpt) REVERT: A 1164 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5580 (m-80) REVERT: B 46 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 373 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7121 (m) REVERT: C 213 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7575 (tp) REVERT: C 215 TRP cc_start: 0.6524 (t-100) cc_final: 0.6246 (t-100) REVERT: C 227 ASP cc_start: 0.7824 (p0) cc_final: 0.7597 (m-30) outliers start: 50 outliers final: 21 residues processed: 176 average time/residue: 0.4155 time to fit residues: 83.0259 Evaluate side-chains 172 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 17 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.148636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.118470 restraints weight = 23912.915| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.89 r_work: 0.3828 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14260 Z= 0.125 Angle : 0.560 9.255 19513 Z= 0.284 Chirality : 0.040 0.184 2132 Planarity : 0.004 0.049 2347 Dihedral : 14.269 84.854 2218 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.26 % Allowed : 17.94 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.22), residues: 1583 helix: 1.52 (0.21), residues: 644 sheet: -0.48 (0.36), residues: 221 loop : 0.16 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 370 TYR 0.024 0.001 TYR C 167 PHE 0.012 0.001 PHE C 119 TRP 0.020 0.001 TRP A 748 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14260) covalent geometry : angle 0.55980 / 0.28 (19513) hydrogen bonds : bond 0.03422 / 2.42 ( 616) hydrogen bonds : angle 4.98211 / 3.52 ( 1699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: A 248 GLU cc_start: 0.4540 (OUTLIER) cc_final: 0.4090 (mt-10) REVERT: A 299 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6881 (mpp) REVERT: A 358 GLU cc_start: 0.7016 (mp0) cc_final: 0.6813 (mp0) REVERT: A 556 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7971 (t) REVERT: A 740 ASN cc_start: 0.7219 (m-40) cc_final: 0.6963 (p0) REVERT: A 919 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6715 (mtt) REVERT: A 985 MET cc_start: 0.6381 (tmm) cc_final: 0.5939 (tmm) REVERT: A 1064 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6492 (tp) REVERT: A 1136 GLU cc_start: 0.7635 (mp0) cc_final: 0.7155 (mp0) REVERT: A 1153 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 1163 MET cc_start: 0.6663 (tpt) cc_final: 0.5751 (tpt) REVERT: A 1164 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5588 (m-80) REVERT: B 46 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 373 CYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7143 (m) REVERT: C 96 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7547 (mmt-90) REVERT: C 215 TRP cc_start: 0.6673 (t-100) cc_final: 0.6381 (t-100) REVERT: C 227 ASP cc_start: 0.7898 (p0) cc_final: 0.7653 (m-30) REVERT: C 409 MET cc_start: 0.7761 (mtp) cc_final: 0.7396 (mtp) outliers start: 46 outliers final: 21 residues processed: 178 average time/residue: 0.4402 time to fit residues: 88.4425 Evaluate side-chains 180 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 163 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 131 optimal weight: 0.0070 chunk 26 optimal weight: 6.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.148789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.118933 restraints weight = 23754.637| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.83 r_work: 0.3841 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14260 Z= 0.127 Angle : 0.564 9.791 19513 Z= 0.285 Chirality : 0.040 0.144 2132 Planarity : 0.004 0.047 2347 Dihedral : 14.232 86.129 2218 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 18.51 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.91 (0.22), residues: 1583 helix: 1.59 (0.21), residues: 644 sheet: -0.51 (0.36), residues: 221 loop : 0.18 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 370 TYR 0.027 0.001 TYR C 406 PHE 0.016 0.001 PHE A 307 TRP 0.020 0.001 TRP A 748 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14260) covalent geometry : angle 0.56393 / 0.29 (19513) hydrogen bonds : bond 0.03394 / 2.40 ( 616) hydrogen bonds : angle 4.92174 / 3.48 ( 1699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 248 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.4131 (mt-10) REVERT: A 299 MET cc_start: 0.7112 (mpp) cc_final: 0.6860 (mpp) REVERT: A 556 THR cc_start: 0.8250 (p) cc_final: 0.7974 (t) REVERT: A 740 ASN cc_start: 0.7216 (m-40) cc_final: 0.6971 (p0) REVERT: A 919 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6743 (mtt) REVERT: A 985 MET cc_start: 0.6414 (tmm) cc_final: 0.5888 (tmm) REVERT: A 1064 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6457 (tp) REVERT: A 1153 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7557 (mt) REVERT: A 1163 MET cc_start: 0.6622 (tpt) cc_final: 0.5692 (tpt) REVERT: A 1164 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5582 (m-80) REVERT: B 46 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7552 (tt) REVERT: B 373 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7153 (m) REVERT: C 96 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7554 (mmt-90) REVERT: C 215 TRP cc_start: 0.6544 (t-100) cc_final: 0.6281 (t-100) REVERT: C 227 ASP cc_start: 0.7950 (p0) cc_final: 0.7699 (m-30) REVERT: C 266 SER cc_start: 0.7994 (m) cc_final: 0.7527 (p) REVERT: C 409 MET cc_start: 0.7768 (mtp) cc_final: 0.7406 (mtp) outliers start: 38 outliers final: 21 residues processed: 174 average time/residue: 0.4436 time to fit residues: 87.4252 Evaluate side-chains 173 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 0.0020 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.149740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.119965 restraints weight = 24042.680| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.90 r_work: 0.3861 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14260 Z= 0.116 Angle : 0.569 11.224 19513 Z= 0.285 Chirality : 0.040 0.146 2132 Planarity : 0.004 0.046 2347 Dihedral : 14.190 87.389 2218 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.20 % Allowed : 19.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.96 (0.22), residues: 1583 helix: 1.66 (0.21), residues: 650 sheet: -0.63 (0.36), residues: 228 loop : 0.24 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 370 TYR 0.024 0.001 TYR C 167 PHE 0.014 0.001 PHE A 307 TRP 0.024 0.001 TRP A 748 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14260) covalent geometry : angle 0.56862 / 0.29 (19513) hydrogen bonds : bond 0.03256 / 2.31 ( 616) hydrogen bonds : angle 4.83244 / 3.41 ( 1699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: A 248 GLU cc_start: 0.4448 (OUTLIER) cc_final: 0.3943 (mt-10) REVERT: A 299 MET cc_start: 0.7151 (mpp) cc_final: 0.6884 (mpp) REVERT: A 358 GLU cc_start: 0.7118 (mp0) cc_final: 0.6690 (tp30) REVERT: A 556 THR cc_start: 0.8205 (p) cc_final: 0.7941 (t) REVERT: A 740 ASN cc_start: 0.7171 (m-40) cc_final: 0.6967 (p0) REVERT: A 985 MET cc_start: 0.6302 (tmm) cc_final: 0.5769 (tmm) REVERT: A 1064 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6430 (tp) REVERT: A 1153 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7546 (mt) REVERT: A 1163 MET cc_start: 0.6593 (tpt) cc_final: 0.5657 (tpt) REVERT: A 1164 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5559 (m-80) REVERT: B 46 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7487 (tt) REVERT: B 373 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7141 (m) REVERT: C 96 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7545 (mmt-90) REVERT: C 215 TRP cc_start: 0.6494 (t-100) cc_final: 0.6229 (t-100) REVERT: C 227 ASP cc_start: 0.7932 (p0) cc_final: 0.7695 (m-30) REVERT: C 266 SER cc_start: 0.8039 (m) cc_final: 0.7559 (p) REVERT: C 409 MET cc_start: 0.7729 (mtp) cc_final: 0.7424 (mtp) outliers start: 31 outliers final: 19 residues processed: 170 average time/residue: 0.4824 time to fit residues: 92.1056 Evaluate side-chains 171 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.149099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.119035 restraints weight = 23799.688| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.96 r_work: 0.3838 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14260 Z= 0.131 Angle : 0.587 15.277 19513 Z= 0.292 Chirality : 0.041 0.197 2132 Planarity : 0.004 0.043 2347 Dihedral : 14.180 89.022 2218 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.34 % Allowed : 19.72 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.95 (0.22), residues: 1583 helix: 1.65 (0.21), residues: 646 sheet: -0.56 (0.36), residues: 221 loop : 0.21 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 370 TYR 0.023 0.001 TYR C 167 PHE 0.013 0.001 PHE A 307 TRP 0.023 0.001 TRP A 748 HIS 0.010 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14260) covalent geometry : angle 0.58714 / 0.29 (19513) hydrogen bonds : bond 0.03350 / 2.38 ( 616) hydrogen bonds : angle 4.83856 / 3.41 ( 1699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: A 248 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.4111 (mt-10) REVERT: A 299 MET cc_start: 0.7151 (mpp) cc_final: 0.6878 (mpp) REVERT: A 358 GLU cc_start: 0.7134 (mp0) cc_final: 0.6703 (tp30) REVERT: A 556 THR cc_start: 0.8164 (p) cc_final: 0.7902 (t) REVERT: A 740 ASN cc_start: 0.7080 (m-40) cc_final: 0.6860 (p0) REVERT: A 985 MET cc_start: 0.6349 (tmm) cc_final: 0.5944 (tmm) REVERT: A 1153 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7539 (mt) REVERT: A 1163 MET cc_start: 0.6594 (tpt) cc_final: 0.5700 (tpt) REVERT: A 1164 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: B 46 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7507 (tt) REVERT: B 373 CYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7163 (m) REVERT: C 96 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7579 (mmt-90) REVERT: C 215 TRP cc_start: 0.6468 (t-100) cc_final: 0.6193 (t-100) REVERT: C 227 ASP cc_start: 0.7929 (p0) cc_final: 0.7690 (m-30) REVERT: C 266 SER cc_start: 0.8043 (m) cc_final: 0.7556 (p) REVERT: C 409 MET cc_start: 0.7722 (mtp) cc_final: 0.7408 (mtp) outliers start: 33 outliers final: 21 residues processed: 176 average time/residue: 0.4449 time to fit residues: 88.6117 Evaluate side-chains 174 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 54 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.149576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.119768 restraints weight = 23968.777| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.95 r_work: 0.3810 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14260 Z= 0.156 Angle : 0.608 12.272 19513 Z= 0.304 Chirality : 0.042 0.269 2132 Planarity : 0.004 0.044 2347 Dihedral : 14.196 89.345 2218 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.20 % Allowed : 20.21 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.87 (0.22), residues: 1583 helix: 1.59 (0.21), residues: 648 sheet: -0.62 (0.35), residues: 221 loop : 0.16 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 370 TYR 0.023 0.002 TYR C 167 PHE 0.041 0.002 PHE A 273 TRP 0.024 0.001 TRP A 748 HIS 0.024 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (14260) covalent geometry : angle 0.60755 / 0.30 (19513) hydrogen bonds : bond 0.03538 / 2.52 ( 616) hydrogen bonds : angle 4.89307 / 3.46 ( 1699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4869.00 seconds wall clock time: 83 minutes 34.66 seconds (5014.66 seconds total)