Starting phenix.real_space_refine on Thu Sep 18 03:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_52828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_52828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_52828.map" model { file = "/net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_52828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic3_52828/09_2025/9ic3_52828.cif" } 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-2.0-5805/lib/python3.9/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: 3.50, per 1000 atoms: 0.25 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: 1.47 Conformation dependent library (CDL) restraints added in 581.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.78 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: 2.97 Time building geometry restraints manager: 1.81 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=" O1A DCP A1304 " pdb=" PA DCP A1304 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.00e-02 1.00e+04 1.07e+01 bond pdb=" C6 DCP A1304 " pdb=" N1 DCP A1304 " ideal model delta sigma weight residual 1.375 1.338 0.037 1.20e-02 6.94e+03 9.29e+00 bond pdb=" C4 DCP A1304 " pdb=" C5 DCP A1304 " ideal model delta sigma weight residual 1.426 1.390 0.036 1.20e-02 6.94e+03 9.00e+00 bond pdb=" O1B DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.10e-02 8.26e+03 8.66e+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 - 3.61: 19473 3.61 - 7.23: 38 7.23 - 10.84: 0 10.84 - 14.45: 0 14.45 - 18.06: 2 Bond angle restraints: 19513 Sorted by residual: angle pdb=" PB DCP A1304 " pdb=" O3B DCP A1304 " pdb=" PG DCP A1304 " ideal model delta sigma weight residual 139.87 121.81 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA DCP A1304 " pdb=" O3A DCP A1304 " pdb=" PB DCP A1304 " ideal model delta sigma weight residual 136.83 120.07 16.76 1.00e+00 1.00e+00 2.81e+02 angle pdb=" O1G DCP A1304 " pdb=" PG DCP A1304 " pdb=" O3B DCP A1304 " ideal model delta sigma weight residual 110.47 103.86 6.61 1.64e+00 3.70e-01 1.62e+01 angle pdb=" N VAL A 196 " pdb=" CA VAL A 196 " pdb=" C VAL A 196 " ideal model delta sigma weight residual 109.80 105.00 4.80 1.33e+00 5.65e-01 1.30e+01 angle pdb=" C2' DCP A1304 " pdb=" C3' DCP A1304 " pdb=" C4' DCP A1304 " ideal model delta sigma weight residual 102.59 106.22 -3.63 1.02e+00 9.67e-01 1.28e+01 ... (remaining 19508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7638 17.44 - 34.89: 527 34.89 - 52.33: 174 52.33 - 69.77: 42 69.77 - 87.22: 1 Dihedral angle restraints: 8382 sinusoidal: 3693 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 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1323 0.029 - 0.057: 546 0.057 - 0.086: 143 0.086 - 0.114: 99 0.114 - 0.143: 21 Chirality restraints: 2132 Sorted by residual: 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 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-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: 2.520 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14260 Z= 0.179 Angle : 0.563 18.064 19513 Z= 0.344 Chirality : 0.038 0.143 2132 Planarity : 0.004 0.041 2347 Dihedral : 13.624 87.216 5344 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 aren 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 covalent geometry : bond 0.00330 (14260) covalent geometry : angle 0.56301 (19513) hydrogen bonds : bond 0.17973 ( 616) hydrogen bonds : angle 7.48387 ( 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 : 0.536 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: 0.5553 time to fit residues: 170.2248 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 : 0.533 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 398 GLN A 550 GLN A 811 GLN A1059 ASN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4422 r_free = 0.4422 target = 0.147885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118374 restraints weight = 23941.586| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.83 r_work: 0.3828 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14260 Z= 0.142 Angle : 0.590 10.829 19513 Z= 0.298 Chirality : 0.041 0.162 2132 Planarity : 0.005 0.042 2347 Dihedral : 14.180 72.695 2219 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.20 % Allowed : 14.04 % Favored : 83.76 % 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 aren not related in a simple way. whole: 0.72 (0.22), residues: 1583 helix: 1.26 (0.21), residues: 651 sheet: -0.30 (0.37), residues: 212 loop : 0.13 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 49 TYR 0.018 0.001 TYR C 167 PHE 0.022 0.001 PHE A 961 TRP 0.025 0.001 TRP B 215 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00309 (14260) covalent geometry : angle 0.59014 (19513) hydrogen bonds : bond 0.04232 ( 616) hydrogen bonds : angle 5.54283 ( 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 209 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.4159 (mt-10) REVERT: A 465 ASP cc_start: 0.7866 (m-30) cc_final: 0.7636 (m-30) REVERT: A 556 THR cc_start: 0.8327 (p) cc_final: 0.8005 (t) REVERT: A 740 ASN cc_start: 0.7345 (m-40) cc_final: 0.7041 (p0) REVERT: A 1064 ILE cc_start: 0.6566 (tp) cc_final: 0.6363 (tp) REVERT: A 1136 GLU cc_start: 0.7585 (mp0) cc_final: 0.7183 (mp0) REVERT: A 1164 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.5496 (m-80) REVERT: B 373 CYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7126 (m) REVERT: C 215 TRP cc_start: 0.6438 (t-100) cc_final: 0.6203 (t-100) REVERT: C 227 ASP cc_start: 0.7905 (p0) cc_final: 0.7583 (m-30) outliers start: 31 outliers final: 11 residues processed: 195 average time/residue: 0.4968 time to fit residues: 108.6565 Evaluate side-chains 156 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 130 optimal weight: 0.0070 chunk 68 optimal weight: 0.3980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.148221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118468 restraints weight = 24073.491| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.90 r_work: 0.3821 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14260 Z= 0.133 Angle : 0.553 11.146 19513 Z= 0.278 Chirality : 0.040 0.141 2132 Planarity : 0.004 0.045 2347 Dihedral : 14.065 77.747 2211 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.12 % Allowed : 14.89 % Favored : 81.99 % 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 aren not related in a simple way. whole: 0.86 (0.22), residues: 1583 helix: 1.38 (0.21), residues: 646 sheet: -0.29 (0.37), residues: 219 loop : 0.25 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 546 TYR 0.021 0.001 TYR C 167 PHE 0.017 0.001 PHE A 273 TRP 0.014 0.001 TRP A 748 HIS 0.004 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00304 (14260) covalent geometry : angle 0.55342 (19513) hydrogen bonds : bond 0.03624 ( 616) hydrogen bonds : angle 5.15122 ( 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 212 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: A 248 GLU cc_start: 0.4592 (OUTLIER) cc_final: 0.4207 (mt-10) REVERT: A 382 MET cc_start: 0.6436 (tmm) cc_final: 0.6236 (tmm) REVERT: A 541 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.5334 (mt0) REVERT: A 556 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7977 (t) REVERT: A 740 ASN cc_start: 0.7284 (m-40) cc_final: 0.7034 (p0) REVERT: A 919 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6839 (mtt) REVERT: A 1064 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6485 (tp) REVERT: A 1136 GLU cc_start: 0.7587 (mp0) cc_final: 0.7136 (mp0) REVERT: A 1164 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: B 373 CYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7146 (m) REVERT: C 215 TRP cc_start: 0.6459 (t-100) cc_final: 0.6191 (t-100) REVERT: C 227 ASP cc_start: 0.7806 (p0) cc_final: 0.7488 (m-30) REVERT: C 254 ASP cc_start: 0.6612 (t0) cc_final: 0.6142 (t0) REVERT: C 409 MET cc_start: 0.7826 (mtp) cc_final: 0.7466 (mtp) outliers start: 44 outliers final: 16 residues processed: 195 average time/residue: 0.4960 time to fit residues: 108.4615 Evaluate side-chains 169 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 541 GLN 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 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 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 217 THR 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: 0.9980 chunk 128 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4407 r_free = 0.4407 target = 0.146708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116337 restraints weight = 24017.058| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.96 r_work: 0.3778 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14260 Z= 0.185 Angle : 0.589 9.439 19513 Z= 0.294 Chirality : 0.041 0.147 2132 Planarity : 0.005 0.053 2347 Dihedral : 14.091 80.971 2211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.11 % Allowed : 14.89 % Favored : 80.99 % 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 aren not related in a simple way. whole: 0.75 (0.22), residues: 1583 helix: 1.39 (0.20), residues: 644 sheet: -0.50 (0.36), residues: 223 loop : 0.15 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 233 TYR 0.021 0.002 TYR C 167 PHE 0.015 0.002 PHE A 273 TRP 0.013 0.001 TRP A 748 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00438 (14260) covalent geometry : angle 0.58864 (19513) hydrogen bonds : bond 0.03760 ( 616) hydrogen bonds : angle 5.15976 ( 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 211 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: A 248 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4175 (mt-10) REVERT: A 740 ASN cc_start: 0.7214 (m-40) cc_final: 0.6930 (p0) REVERT: A 919 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6809 (mtt) REVERT: A 1064 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6653 (tp) REVERT: A 1153 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 1164 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: B 373 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7155 (m) REVERT: C 213 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7514 (tp) REVERT: C 227 ASP cc_start: 0.7840 (p0) cc_final: 0.7511 (m-30) outliers start: 58 outliers final: 22 residues processed: 187 average time/residue: 0.4615 time to fit residues: 97.6150 Evaluate side-chains 174 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 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 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 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 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 274 ILE 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: 0.0050 chunk 145 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4410 r_free = 0.4410 target = 0.147051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.117006 restraints weight = 24116.810| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.85 r_work: 0.3794 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14260 Z= 0.155 Angle : 0.564 8.865 19513 Z= 0.283 Chirality : 0.040 0.144 2132 Planarity : 0.004 0.051 2347 Dihedral : 14.045 82.195 2211 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.19 % Allowed : 16.60 % Favored : 80.21 % 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 aren not related in a simple way. whole: 0.82 (0.22), residues: 1583 helix: 1.48 (0.21), residues: 644 sheet: -0.52 (0.36), residues: 223 loop : 0.17 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 370 TYR 0.023 0.002 TYR C 167 PHE 0.013 0.001 PHE A 273 TRP 0.017 0.001 TRP A 748 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00366 (14260) covalent geometry : angle 0.56381 (19513) hydrogen bonds : bond 0.03496 ( 616) hydrogen bonds : angle 5.04398 ( 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 197 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: A 248 GLU cc_start: 0.4573 (OUTLIER) cc_final: 0.4097 (mt-10) REVERT: A 556 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7959 (t) REVERT: A 919 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6798 (mtt) REVERT: A 1064 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6616 (tp) REVERT: A 1153 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 1163 MET cc_start: 0.6615 (tpt) cc_final: 0.5727 (tpt) REVERT: A 1164 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.5572 (m-80) REVERT: B 373 CYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7133 (m) REVERT: C 213 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7565 (tp) REVERT: C 227 ASP cc_start: 0.7853 (p0) cc_final: 0.7568 (m-30) REVERT: C 409 MET cc_start: 0.7852 (mtp) cc_final: 0.7501 (mtp) outliers start: 45 outliers final: 26 residues processed: 178 average time/residue: 0.4608 time to fit residues: 92.7231 Evaluate side-chains 176 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 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 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 357 VAL Chi-restraints excluded: chain C residue 360 ASP 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: 0.7980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 811 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 = 0.4410 r_free = 0.4410 target = 0.146919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.117090 restraints weight = 23859.432| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.81 r_work: 0.3804 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14260 Z= 0.163 Angle : 0.572 9.938 19513 Z= 0.286 Chirality : 0.040 0.144 2132 Planarity : 0.004 0.052 2347 Dihedral : 14.017 83.716 2211 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.76 % Allowed : 16.95 % Favored : 79.29 % 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 aren not related in a simple way. whole: 0.77 (0.22), residues: 1583 helix: 1.42 (0.21), residues: 651 sheet: -0.50 (0.36), residues: 221 loop : 0.13 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 370 TYR 0.023 0.002 TYR C 167 PHE 0.012 0.001 PHE B 267 TRP 0.025 0.001 TRP C 215 HIS 0.005 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00386 (14260) covalent geometry : angle 0.57170 (19513) hydrogen bonds : bond 0.03510 ( 616) hydrogen bonds : angle 5.02352 ( 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 203 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: A 248 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.3992 (mt-10) REVERT: A 299 MET cc_start: 0.7106 (mpp) cc_final: 0.6845 (mpp) REVERT: A 358 GLU cc_start: 0.7116 (mp0) cc_final: 0.6737 (tp30) REVERT: A 919 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6828 (mtt) REVERT: A 1064 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6653 (tp) REVERT: A 1153 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7581 (mt) REVERT: A 1163 MET cc_start: 0.6632 (tpt) cc_final: 0.5772 (tpt) REVERT: A 1164 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: B 46 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7594 (tt) REVERT: B 373 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7141 (m) REVERT: C 213 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7674 (tp) REVERT: C 215 TRP cc_start: 0.6343 (t-100) cc_final: 0.5926 (t-100) REVERT: C 227 ASP cc_start: 0.7920 (p0) cc_final: 0.7663 (m-30) REVERT: C 266 SER cc_start: 0.7971 (m) cc_final: 0.7512 (p) REVERT: C 409 MET cc_start: 0.7815 (mtp) cc_final: 0.7493 (mtp) outliers start: 53 outliers final: 27 residues processed: 186 average time/residue: 0.4642 time to fit residues: 97.6550 Evaluate side-chains 181 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 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 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 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 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 46 LEU Chi-restraints excluded: chain C residue 213 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4415 r_free = 0.4415 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.117497 restraints weight = 23886.031| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.80 r_work: 0.3815 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2494 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= 0.155 Angle : 0.576 13.149 19513 Z= 0.285 Chirality : 0.040 0.145 2132 Planarity : 0.004 0.050 2347 Dihedral : 13.991 84.955 2211 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.40 % Allowed : 17.73 % Favored : 78.87 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1583 helix: 1.42 (0.21), residues: 651 sheet: -0.53 (0.36), residues: 221 loop : 0.13 (0.24), residues: 711 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 0.012 0.001 PHE B 267 TRP 0.017 0.001 TRP A 748 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00367 (14260) covalent geometry : angle 0.57609 (19513) hydrogen bonds : bond 0.03497 ( 616) hydrogen bonds : angle 4.98601 ( 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: 48 poor density : 150 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 248 GLU cc_start: 0.4508 (OUTLIER) cc_final: 0.3945 (mt-10) REVERT: A 299 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6870 (mpp) REVERT: A 358 GLU cc_start: 0.7034 (mp0) cc_final: 0.6646 (tp30) REVERT: A 910 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4566 (ptp) REVERT: A 951 TYR cc_start: 0.5929 (m-80) cc_final: 0.5724 (m-80) REVERT: A 1064 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6694 (tp) REVERT: A 1153 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 1163 MET cc_start: 0.6669 (tpt) cc_final: 0.5742 (tpt) REVERT: A 1164 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.5638 (m-80) REVERT: B 46 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7569 (tt) REVERT: B 373 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7143 (m) REVERT: C 213 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7698 (tp) REVERT: C 215 TRP cc_start: 0.6347 (t-100) cc_final: 0.5990 (t-100) REVERT: C 227 ASP cc_start: 0.7876 (p0) cc_final: 0.7657 (m-30) REVERT: C 266 SER cc_start: 0.7987 (m) cc_final: 0.7531 (p) outliers start: 48 outliers final: 26 residues processed: 179 average time/residue: 0.5015 time to fit residues: 100.7028 Evaluate side-chains 180 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 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 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 274 ILE 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: 0.6980 chunk 65 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 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 = 0.4391 r_free = 0.4391 target = 0.145751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.116015 restraints weight = 23809.559| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.83 r_work: 0.3773 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14260 Z= 0.225 Angle : 0.637 12.840 19513 Z= 0.317 Chirality : 0.043 0.181 2132 Planarity : 0.005 0.048 2347 Dihedral : 14.082 87.157 2211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.19 % Allowed : 18.37 % Favored : 78.44 % 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 aren not related in a simple way. whole: 0.53 (0.22), residues: 1583 helix: 1.23 (0.20), residues: 651 sheet: -0.69 (0.35), residues: 230 loop : 0.01 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 370 TYR 0.023 0.002 TYR C 167 PHE 0.016 0.002 PHE B 267 TRP 0.017 0.002 TRP A 748 HIS 0.007 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00536 (14260) covalent geometry : angle 0.63734 (19513) hydrogen bonds : bond 0.03878 ( 616) hydrogen bonds : angle 5.18648 ( 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 189 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 248 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.4098 (mt-10) REVERT: A 299 MET cc_start: 0.7149 (mpp) cc_final: 0.6877 (mpp) REVERT: A 358 GLU cc_start: 0.6993 (mp0) cc_final: 0.6552 (tp30) REVERT: A 910 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4542 (ptp) REVERT: A 1064 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6743 (tp) REVERT: A 1153 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 1163 MET cc_start: 0.6543 (tpt) cc_final: 0.5680 (tpt) REVERT: A 1164 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.5591 (m-80) REVERT: B 46 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7598 (tt) REVERT: B 373 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7082 (m) REVERT: C 215 TRP cc_start: 0.6453 (t-100) cc_final: 0.6062 (t-100) REVERT: C 227 ASP cc_start: 0.7926 (p0) cc_final: 0.7706 (m-30) REVERT: C 409 MET cc_start: 0.7870 (mtp) cc_final: 0.7467 (mtp) outliers start: 45 outliers final: 25 residues processed: 172 average time/residue: 0.4862 time to fit residues: 93.7972 Evaluate side-chains 169 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 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 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 274 ILE Chi-restraints excluded: chain C residue 357 VAL 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: 10.0000 chunk 151 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.147687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.117960 restraints weight = 23969.864| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.75 r_work: 0.3817 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14260 Z= 0.146 Angle : 0.600 13.676 19513 Z= 0.298 Chirality : 0.041 0.145 2132 Planarity : 0.004 0.047 2347 Dihedral : 13.998 88.155 2211 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.62 % Allowed : 19.22 % Favored : 78.16 % 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 aren not related in a simple way. whole: 0.69 (0.22), residues: 1583 helix: 1.38 (0.21), residues: 652 sheet: -0.59 (0.35), residues: 218 loop : 0.07 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 370 TYR 0.024 0.002 TYR C 167 PHE 0.014 0.001 PHE C 119 TRP 0.023 0.001 TRP A 748 HIS 0.008 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00344 (14260) covalent geometry : angle 0.59988 (19513) hydrogen bonds : bond 0.03413 ( 616) hydrogen bonds : angle 5.00037 ( 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 186 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: A 248 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.3911 (mt-10) REVERT: A 299 MET cc_start: 0.7173 (mpp) cc_final: 0.6918 (mpp) REVERT: A 358 GLU cc_start: 0.7008 (mp0) cc_final: 0.6534 (tp30) REVERT: A 1054 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7473 (mt-10) REVERT: A 1153 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 1163 MET cc_start: 0.6530 (tpt) cc_final: 0.5636 (tpt) REVERT: A 1164 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5545 (m-80) REVERT: B 46 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7547 (tt) REVERT: C 96 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7561 (mmt-90) REVERT: C 215 TRP cc_start: 0.6214 (t-100) cc_final: 0.5828 (t-100) REVERT: C 227 ASP cc_start: 0.7966 (p0) cc_final: 0.7721 (m-30) REVERT: C 266 SER cc_start: 0.7951 (m) cc_final: 0.7484 (p) REVERT: C 409 MET cc_start: 0.7805 (mtp) cc_final: 0.7470 (mtp) outliers start: 37 outliers final: 23 residues processed: 171 average time/residue: 0.5424 time to fit residues: 103.1711 Evaluate side-chains 171 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 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 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 274 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 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 = 0.4457 r_free = 0.4457 target = 0.150193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.120935 restraints weight = 23755.124| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.76 r_work: 0.3844 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14260 Z= 0.126 Angle : 0.593 14.994 19513 Z= 0.293 Chirality : 0.040 0.146 2132 Planarity : 0.004 0.045 2347 Dihedral : 13.916 89.302 2211 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.06 % Allowed : 20.07 % Favored : 77.87 % 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 aren not related in a simple way. whole: 0.81 (0.22), residues: 1583 helix: 1.53 (0.21), residues: 648 sheet: -0.65 (0.35), residues: 230 loop : 0.14 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 370 TYR 0.024 0.001 TYR C 167 PHE 0.033 0.001 PHE A 961 TRP 0.021 0.001 TRP A 748 HIS 0.012 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00293 (14260) covalent geometry : angle 0.59289 (19513) hydrogen bonds : bond 0.03304 ( 616) hydrogen bonds : angle 4.90145 ( 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 182 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: A 248 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.3872 (mt-10) REVERT: A 299 MET cc_start: 0.7121 (mpp) cc_final: 0.6864 (mpp) REVERT: A 358 GLU cc_start: 0.7004 (mp0) cc_final: 0.6620 (tp30) REVERT: A 1054 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 1153 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 1163 MET cc_start: 0.6463 (tpt) cc_final: 0.5565 (tpt) REVERT: A 1164 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: B 46 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7512 (tt) REVERT: B 373 CYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7068 (m) REVERT: C 96 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7559 (mmt-90) REVERT: C 215 TRP cc_start: 0.6187 (t-100) cc_final: 0.5832 (t-100) REVERT: C 227 ASP cc_start: 0.7965 (p0) cc_final: 0.7740 (m-30) REVERT: C 266 SER cc_start: 0.7949 (m) cc_final: 0.7435 (p) REVERT: C 409 MET cc_start: 0.7809 (mtp) cc_final: 0.7466 (mtp) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 0.4942 time to fit residues: 95.1740 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 : 0.504 ------------------------------------------------------------------------------- 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 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 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 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 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 357 VAL Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4423 r_free = 0.4423 target = 0.148050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.118404 restraints weight = 23898.188| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.78 r_work: 0.3832 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14260 Z= 0.152 Angle : 0.619 12.261 19513 Z= 0.308 Chirality : 0.041 0.196 2132 Planarity : 0.004 0.046 2347 Dihedral : 13.927 88.869 2211 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.91 % Allowed : 20.92 % Favored : 77.16 % 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 aren not related in a simple way. whole: 0.72 (0.22), residues: 1583 helix: 1.41 (0.21), residues: 654 sheet: -0.65 (0.35), residues: 230 loop : 0.12 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 370 TYR 0.029 0.002 TYR A 955 PHE 0.032 0.002 PHE A 961 TRP 0.020 0.001 TRP A 748 HIS 0.029 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00360 (14260) covalent geometry : angle 0.61949 (19513) hydrogen bonds : bond 0.03493 ( 616) hydrogen bonds : angle 4.94634 ( 1699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5541.16 seconds wall clock time: 95 minutes 7.44 seconds (5707.44 seconds total)