Starting phenix.real_space_refine on Thu Jul 31 19:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic3_52828/07_2025/9ic3_52828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic3_52828/07_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_52828/07_2025/9ic3_52828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic3_52828/07_2025/9ic3_52828.map" model { file = "/net/cci-nas-00/data/ceres_data/9ic3_52828/07_2025/9ic3_52828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic3_52828/07_2025/9ic3_52828.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.164 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.03, per 1000 atoms: 0.58 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.48 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: 4.73 Time building geometry restraints manager: 3.94 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: 0.010 Normalize map: mean=0, sd=1: 1.810 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (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 TRP 0.008 0.001 TRP A1049 HIS 0.003 0.001 HIS B 287 PHE 0.013 0.001 PHE A 389 TYR 0.010 0.001 TYR A 150 ARG 0.003 0.000 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.17973 ( 616) hydrogen bonds : angle 7.48387 ( 1699) covalent geometry : bond 0.00330 (14260) covalent geometry : angle 0.56301 (19513) *********************** 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 : 1.410 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: 1.0972 time to fit residues: 336.8454 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 : 1.458 ------------------------------------------------------------------------------- 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 139 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 0.0010 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 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 = 0.4410 r_free = 0.4410 target = 0.146998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.117353 restraints weight = 23740.316| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.80 r_work: 0.3806 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14260 Z= 0.166 Angle : 0.607 10.960 19513 Z= 0.307 Chirality : 0.041 0.162 2132 Planarity : 0.005 0.045 2347 Dihedral : 14.222 72.986 2219 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.48 % Allowed : 14.11 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1583 helix: 1.16 (0.21), residues: 651 sheet: -0.42 (0.36), residues: 216 loop : 0.06 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 215 HIS 0.006 0.001 HIS B 287 PHE 0.023 0.002 PHE A 961 TYR 0.019 0.002 TYR C 167 ARG 0.006 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 616) hydrogen bonds : angle 5.62015 ( 1699) covalent geometry : bond 0.00383 (14260) covalent geometry : angle 0.60720 (19513) *********************** 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: 35 poor density : 174 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.4188 (mt-10) REVERT: A 290 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.7356 (mmt-90) REVERT: A 465 ASP cc_start: 0.7908 (m-30) cc_final: 0.7671 (m-30) REVERT: A 740 ASN cc_start: 0.7393 (m-40) cc_final: 0.7053 (p0) REVERT: A 1064 ILE cc_start: 0.6691 (tp) cc_final: 0.6479 (tp) REVERT: A 1136 GLU cc_start: 0.7621 (mp0) cc_final: 0.7232 (mp0) REVERT: A 1164 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.5525 (m-80) REVERT: B 373 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7119 (m) REVERT: C 215 TRP cc_start: 0.6447 (t-100) cc_final: 0.6217 (t-100) REVERT: C 227 ASP cc_start: 0.7932 (p0) cc_final: 0.7605 (m-30) outliers start: 35 outliers final: 15 residues processed: 195 average time/residue: 1.0063 time to fit residues: 221.6330 Evaluate side-chains 158 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 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 348 LEU 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 447 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.147983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118319 restraints weight = 23896.084| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.87 r_work: 0.3823 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14260 Z= 0.134 Angle : 0.559 10.928 19513 Z= 0.280 Chirality : 0.040 0.144 2132 Planarity : 0.004 0.046 2347 Dihedral : 14.160 77.735 2213 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.12 % Allowed : 14.82 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1583 helix: 1.33 (0.21), residues: 646 sheet: -0.33 (0.37), residues: 214 loop : 0.19 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 215 HIS 0.004 0.001 HIS B 287 PHE 0.017 0.001 PHE A 961 TYR 0.021 0.001 TYR C 167 ARG 0.005 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 616) hydrogen bonds : angle 5.23652 ( 1699) covalent geometry : bond 0.00306 (14260) covalent geometry : angle 0.55877 (19513) *********************** 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 211 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 248 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4204 (mt-10) REVERT: A 290 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.7313 (mmt-90) REVERT: A 465 ASP cc_start: 0.7886 (m-30) cc_final: 0.7685 (m-30) REVERT: A 541 GLN cc_start: 0.5548 (OUTLIER) cc_final: 0.5344 (mt0) REVERT: A 556 THR cc_start: 0.8318 (p) cc_final: 0.8002 (t) REVERT: A 580 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6757 (tt) REVERT: A 740 ASN cc_start: 0.7301 (m-40) cc_final: 0.7045 (p0) REVERT: A 919 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: A 1064 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6500 (tp) REVERT: A 1136 GLU cc_start: 0.7608 (mp0) cc_final: 0.7179 (mp0) REVERT: A 1153 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 1164 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: B 373 CYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7144 (m) REVERT: C 215 TRP cc_start: 0.6444 (t-100) cc_final: 0.6157 (t-100) REVERT: C 227 ASP cc_start: 0.7790 (p0) cc_final: 0.7486 (m-30) REVERT: C 310 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7474 (pt) outliers start: 44 outliers final: 14 residues processed: 195 average time/residue: 0.9631 time to fit residues: 211.1812 Evaluate side-chains 167 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 81 optimal weight: 0.0040 chunk 43 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.148360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.118610 restraints weight = 23847.550| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.86 r_work: 0.3818 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14260 Z= 0.131 Angle : 0.549 8.631 19513 Z= 0.274 Chirality : 0.040 0.149 2132 Planarity : 0.004 0.051 2347 Dihedral : 14.097 79.610 2213 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.26 % Allowed : 15.32 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1583 helix: 1.49 (0.21), residues: 642 sheet: -0.34 (0.37), residues: 214 loop : 0.22 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 748 HIS 0.005 0.001 HIS C 232 PHE 0.016 0.001 PHE A 307 TYR 0.022 0.001 TYR C 167 ARG 0.004 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 616) hydrogen bonds : angle 5.07396 ( 1699) covalent geometry : bond 0.00305 (14260) covalent geometry : angle 0.54892 (19513) *********************** 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 201 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: A 248 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.4112 (mt-10) REVERT: A 289 MET cc_start: 0.7104 (ttm) cc_final: 0.6877 (ttm) REVERT: A 290 ARG cc_start: 0.7489 (mmt-90) cc_final: 0.7233 (mmt-90) REVERT: A 541 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.5331 (mt0) REVERT: A 556 THR cc_start: 0.8290 (p) cc_final: 0.7981 (t) REVERT: A 580 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6693 (tt) REVERT: A 740 ASN cc_start: 0.7301 (m-40) cc_final: 0.7053 (p0) REVERT: A 919 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6833 (mtt) REVERT: A 1064 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6519 (tp) REVERT: A 1136 GLU cc_start: 0.7619 (mp0) cc_final: 0.7149 (mp0) REVERT: A 1153 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 1164 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5618 (m-80) REVERT: B 373 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7153 (m) REVERT: C 213 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7528 (tp) REVERT: C 215 TRP cc_start: 0.6487 (t-100) cc_final: 0.6207 (t-100) REVERT: C 227 ASP cc_start: 0.7809 (p0) cc_final: 0.7509 (m-30) REVERT: C 254 ASP cc_start: 0.6659 (t0) cc_final: 0.6146 (t0) REVERT: C 310 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7428 (pt) REVERT: C 409 MET cc_start: 0.7842 (mtp) cc_final: 0.7477 (mtp) outliers start: 46 outliers final: 16 residues processed: 182 average time/residue: 0.9401 time to fit residues: 193.6309 Evaluate side-chains 171 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 541 GLN 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 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 213 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.148098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.118211 restraints weight = 23976.464| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.86 r_work: 0.3812 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14260 Z= 0.139 Angle : 0.549 9.764 19513 Z= 0.276 Chirality : 0.040 0.155 2132 Planarity : 0.004 0.050 2347 Dihedral : 13.996 80.758 2211 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.69 % Allowed : 15.82 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1583 helix: 1.53 (0.21), residues: 643 sheet: -0.37 (0.37), residues: 213 loop : 0.24 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 748 HIS 0.005 0.001 HIS B 287 PHE 0.013 0.001 PHE A 273 TYR 0.022 0.001 TYR C 167 ARG 0.004 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 616) hydrogen bonds : angle 4.97585 ( 1699) covalent geometry : bond 0.00324 (14260) covalent geometry : angle 0.54858 (19513) *********************** 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 210 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: A 248 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.4140 (mt-10) REVERT: A 290 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7215 (mmt-90) REVERT: A 541 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.5320 (mt0) REVERT: A 556 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 580 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6778 (tt) REVERT: A 740 ASN cc_start: 0.7250 (m-40) cc_final: 0.7002 (p0) REVERT: A 910 MET cc_start: 0.5279 (OUTLIER) cc_final: 0.4452 (ptp) REVERT: A 919 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6816 (mtt) REVERT: A 1057 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.4612 (tmm) REVERT: A 1064 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6562 (tp) REVERT: A 1136 GLU cc_start: 0.7617 (mp0) cc_final: 0.7175 (mp0) REVERT: A 1153 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 1163 MET cc_start: 0.6714 (tpt) cc_final: 0.5804 (tpt) REVERT: A 1164 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.5588 (m-80) REVERT: B 373 CYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7157 (m) REVERT: C 96 ARG cc_start: 0.8205 (tpp-160) cc_final: 0.7556 (mmt-90) REVERT: C 213 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7500 (tp) REVERT: C 215 TRP cc_start: 0.6582 (t-100) cc_final: 0.6263 (t-100) REVERT: C 227 ASP cc_start: 0.7817 (p0) cc_final: 0.7511 (m-30) REVERT: C 310 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7407 (pt) outliers start: 52 outliers final: 20 residues processed: 189 average time/residue: 0.9351 time to fit residues: 199.8325 Evaluate side-chains 178 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 454 GLU 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 792 LEU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 386 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 0.0050 chunk 147 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 155 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6332 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.149229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.119512 restraints weight = 24089.369| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.83 r_work: 0.3840 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14260 Z= 0.119 Angle : 0.546 12.196 19513 Z= 0.271 Chirality : 0.039 0.145 2132 Planarity : 0.004 0.049 2347 Dihedral : 13.925 81.603 2211 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 16.81 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1583 helix: 1.66 (0.21), residues: 644 sheet: -0.43 (0.36), residues: 221 loop : 0.27 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 748 HIS 0.005 0.001 HIS B 287 PHE 0.013 0.001 PHE C 119 TYR 0.024 0.001 TYR C 167 ARG 0.010 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 616) hydrogen bonds : angle 4.84617 ( 1699) covalent geometry : bond 0.00275 (14260) covalent geometry : angle 0.54637 (19513) *********************** 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 198 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: A 248 GLU cc_start: 0.4545 (OUTLIER) cc_final: 0.4035 (mt-10) REVERT: A 290 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.7093 (mmt-90) REVERT: A 556 THR cc_start: 0.8207 (p) cc_final: 0.7943 (t) REVERT: A 580 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6671 (tt) REVERT: A 740 ASN cc_start: 0.7233 (m-40) cc_final: 0.7020 (p0) REVERT: A 919 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: A 1064 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6431 (tp) REVERT: A 1136 GLU cc_start: 0.7540 (mp0) cc_final: 0.7055 (mp0) REVERT: A 1153 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7516 (mt) REVERT: A 1163 MET cc_start: 0.6652 (tpt) cc_final: 0.5760 (tpt) REVERT: A 1164 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: B 46 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7548 (tt) REVERT: B 97 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7040 (tp30) REVERT: B 373 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7130 (m) REVERT: C 96 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7543 (mmt-90) REVERT: C 213 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7541 (tp) REVERT: C 215 TRP cc_start: 0.6476 (t-100) cc_final: 0.6125 (t-100) REVERT: C 227 ASP cc_start: 0.7882 (p0) cc_final: 0.7603 (m-30) REVERT: C 266 SER cc_start: 0.7991 (m) cc_final: 0.7518 (p) REVERT: C 409 MET cc_start: 0.7818 (mtp) cc_final: 0.7430 (mtp) outliers start: 45 outliers final: 23 residues processed: 184 average time/residue: 0.9707 time to fit residues: 201.9201 Evaluate side-chains 181 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 949 PHE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 427 ILE 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 147 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.118889 restraints weight = 24009.410| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.92 r_work: 0.3828 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2569 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= 0.131 Angle : 0.558 11.741 19513 Z= 0.277 Chirality : 0.040 0.159 2132 Planarity : 0.004 0.044 2347 Dihedral : 13.910 82.528 2211 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 17.59 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1583 helix: 1.69 (0.21), residues: 645 sheet: -0.51 (0.36), residues: 221 loop : 0.25 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 748 HIS 0.006 0.001 HIS C 232 PHE 0.012 0.001 PHE A 389 TYR 0.023 0.001 TYR C 167 ARG 0.008 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 616) hydrogen bonds : angle 4.82150 ( 1699) covalent geometry : bond 0.00308 (14260) covalent geometry : angle 0.55846 (19513) *********************** 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 202 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 248 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.4009 (mt-10) REVERT: A 290 ARG cc_start: 0.7404 (mmt-90) cc_final: 0.7104 (mmt-90) REVERT: A 556 THR cc_start: 0.8211 (p) cc_final: 0.7940 (t) REVERT: A 580 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6759 (tt) REVERT: A 740 ASN cc_start: 0.7252 (m-40) cc_final: 0.7030 (p0) REVERT: A 919 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6798 (mtt) REVERT: A 1064 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6468 (tp) REVERT: A 1136 GLU cc_start: 0.7567 (mp0) cc_final: 0.7066 (mp0) REVERT: A 1153 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7548 (mt) REVERT: A 1163 MET cc_start: 0.6649 (tpt) cc_final: 0.5735 (tpt) REVERT: A 1164 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5573 (m-80) REVERT: B 46 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7556 (tt) REVERT: B 97 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7062 (tp30) REVERT: B 373 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7148 (m) REVERT: C 96 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7566 (mmt-90) REVERT: C 213 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7558 (tp) REVERT: C 215 TRP cc_start: 0.6623 (t-100) cc_final: 0.6348 (t-100) REVERT: C 227 ASP cc_start: 0.7901 (p0) cc_final: 0.7631 (m-30) REVERT: C 266 SER cc_start: 0.8027 (m) cc_final: 0.7555 (p) REVERT: C 409 MET cc_start: 0.7758 (mtp) cc_final: 0.7392 (mtp) outliers start: 45 outliers final: 24 residues processed: 186 average time/residue: 1.0056 time to fit residues: 210.0178 Evaluate side-chains 182 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 949 PHE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain 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 B residue 427 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 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 15 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.149062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.119302 restraints weight = 23859.220| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.87 r_work: 0.3830 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14260 Z= 0.131 Angle : 0.567 13.398 19513 Z= 0.281 Chirality : 0.040 0.184 2132 Planarity : 0.004 0.044 2347 Dihedral : 13.893 83.533 2211 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.98 % Allowed : 18.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1583 helix: 1.71 (0.21), residues: 646 sheet: -0.66 (0.35), residues: 230 loop : 0.26 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 175 HIS 0.007 0.001 HIS C 232 PHE 0.032 0.001 PHE A 961 TYR 0.025 0.001 TYR C 406 ARG 0.008 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 616) hydrogen bonds : angle 4.80806 ( 1699) covalent geometry : bond 0.00307 (14260) covalent geometry : angle 0.56681 (19513) *********************** 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 199 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: A 248 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.3981 (mt-10) REVERT: A 290 ARG cc_start: 0.7393 (mmt-90) cc_final: 0.7057 (mmt-90) REVERT: A 358 GLU cc_start: 0.7154 (mp0) cc_final: 0.6786 (tp30) REVERT: A 556 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7941 (t) REVERT: A 580 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6756 (tt) REVERT: A 740 ASN cc_start: 0.7249 (m-40) cc_final: 0.7011 (p0) REVERT: A 910 MET cc_start: 0.5327 (OUTLIER) cc_final: 0.4495 (ptp) REVERT: A 919 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6810 (mtt) REVERT: A 951 TYR cc_start: 0.5898 (m-80) cc_final: 0.5688 (m-80) REVERT: A 1064 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6500 (tp) REVERT: A 1136 GLU cc_start: 0.7566 (mp0) cc_final: 0.7056 (mp0) REVERT: A 1153 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 1163 MET cc_start: 0.6580 (tpt) cc_final: 0.5724 (tpt) REVERT: A 1164 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: A 1192 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6671 (mp0) REVERT: B 46 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7538 (tt) REVERT: B 97 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7056 (tp30) REVERT: B 373 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7125 (m) REVERT: C 96 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7561 (mmt-90) REVERT: C 213 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7537 (tp) REVERT: C 215 TRP cc_start: 0.6499 (t-100) cc_final: 0.6229 (t-100) REVERT: C 227 ASP cc_start: 0.7868 (p0) cc_final: 0.7627 (m-30) REVERT: C 266 SER cc_start: 0.8029 (m) cc_final: 0.7552 (p) REVERT: C 409 MET cc_start: 0.7689 (mtp) cc_final: 0.7364 (mtp) outliers start: 42 outliers final: 23 residues processed: 184 average time/residue: 0.9351 time to fit residues: 194.6076 Evaluate side-chains 181 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 861 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 949 PHE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain 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 427 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.147044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.116670 restraints weight = 23834.203| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.93 r_work: 0.3762 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14260 Z= 0.195 Angle : 0.613 13.204 19513 Z= 0.305 Chirality : 0.042 0.149 2132 Planarity : 0.004 0.044 2347 Dihedral : 13.974 85.687 2211 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.05 % Allowed : 18.37 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1583 helix: 1.48 (0.20), residues: 652 sheet: -0.74 (0.35), residues: 230 loop : 0.16 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.009 0.001 HIS C 232 PHE 0.028 0.002 PHE A 961 TYR 0.023 0.002 TYR C 167 ARG 0.008 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 616) hydrogen bonds : angle 4.97378 ( 1699) covalent geometry : bond 0.00465 (14260) covalent geometry : angle 0.61277 (19513) *********************** 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 189 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: A 248 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.3956 (mt-10) REVERT: A 358 GLU cc_start: 0.7215 (mp0) cc_final: 0.6796 (tp30) REVERT: A 580 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6805 (tt) REVERT: A 910 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4502 (ptp) REVERT: A 955 TYR cc_start: 0.6839 (m-80) cc_final: 0.6549 (m-80) REVERT: A 1064 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6632 (tp) REVERT: A 1153 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 1163 MET cc_start: 0.6610 (tpt) cc_final: 0.5716 (tpt) REVERT: A 1164 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5553 (m-80) REVERT: B 46 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7560 (tt) REVERT: B 373 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7129 (m) REVERT: C 96 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7619 (mmt-90) REVERT: C 213 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7589 (tp) REVERT: C 227 ASP cc_start: 0.7919 (p0) cc_final: 0.7689 (m-30) REVERT: C 266 SER cc_start: 0.7952 (m) cc_final: 0.7478 (p) outliers start: 43 outliers final: 24 residues processed: 173 average time/residue: 1.1780 time to fit residues: 230.2055 Evaluate side-chains 178 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 121 optimal weight: 0.0570 chunk 137 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.149266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.119677 restraints weight = 23833.916| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.94 r_work: 0.3843 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14260 Z= 0.124 Angle : 0.592 13.694 19513 Z= 0.292 Chirality : 0.040 0.153 2132 Planarity : 0.004 0.043 2347 Dihedral : 13.879 85.840 2211 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 19.57 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1583 helix: 1.67 (0.21), residues: 647 sheet: -0.77 (0.35), residues: 237 loop : 0.24 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 215 HIS 0.013 0.001 HIS C 232 PHE 0.026 0.001 PHE A 961 TYR 0.020 0.001 TYR B 452 ARG 0.007 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 616) hydrogen bonds : angle 4.79732 ( 1699) covalent geometry : bond 0.00289 (14260) covalent geometry : angle 0.59178 (19513) ********************** 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 181 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: A 248 GLU cc_start: 0.4496 (OUTLIER) cc_final: 0.3915 (mt-10) REVERT: A 299 MET cc_start: 0.7067 (mpp) cc_final: 0.6833 (mpp) REVERT: A 358 GLU cc_start: 0.7207 (mp0) cc_final: 0.6790 (tp30) REVERT: A 556 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 580 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6767 (tt) REVERT: A 955 TYR cc_start: 0.6941 (m-80) cc_final: 0.6609 (m-80) REVERT: A 1064 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6589 (tp) REVERT: A 1153 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 1163 MET cc_start: 0.6571 (tpt) cc_final: 0.5673 (tpt) REVERT: A 1164 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: B 46 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7531 (tt) REVERT: B 373 CYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7114 (m) REVERT: C 96 ARG cc_start: 0.8242 (tpp-160) cc_final: 0.7594 (mmt-90) REVERT: C 213 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7547 (tp) REVERT: C 215 TRP cc_start: 0.6293 (t-100) cc_final: 0.5923 (t-100) REVERT: C 227 ASP cc_start: 0.7925 (p0) cc_final: 0.7712 (m-30) REVERT: C 266 SER cc_start: 0.8043 (m) cc_final: 0.7529 (p) REVERT: C 296 ILE cc_start: 0.4717 (mm) cc_final: 0.4397 (mt) outliers start: 30 outliers final: 19 residues processed: 171 average time/residue: 0.9905 time to fit residues: 190.6072 Evaluate side-chains 176 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 861 THR 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 46 LEU Chi-restraints excluded: chain C residue 213 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 54 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.149201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.119529 restraints weight = 24079.447| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.98 r_work: 0.3819 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14260 Z= 0.133 Angle : 0.600 14.259 19513 Z= 0.296 Chirality : 0.040 0.200 2132 Planarity : 0.004 0.044 2347 Dihedral : 13.860 86.740 2211 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.27 % Allowed : 19.65 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1583 helix: 1.67 (0.21), residues: 647 sheet: -0.63 (0.35), residues: 229 loop : 0.20 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 215 HIS 0.024 0.001 HIS C 232 PHE 0.032 0.001 PHE C 228 TYR 0.023 0.002 TYR C 406 ARG 0.007 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 616) hydrogen bonds : angle 4.77855 ( 1699) covalent geometry : bond 0.00313 (14260) covalent geometry : angle 0.59963 (19513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10832.52 seconds wall clock time: 190 minutes 35.96 seconds (11435.96 seconds total)